Blood-Brain Barrier Targeting Anti-bodies

ABSTRACT

This invention provides antibodies that bind brain endothelial cell receptors resulting in endocytosis/transcytosis of the receptor and bound ligands. In some embodiments, the ligand comprises the antibody in combination with a pharmaceutically active compound and the antibody directs delivery of the compound across the blood brain barrier (BBB). The invention also provides methods of identifying endothelial cell specific antibodies by panning the library against cultured cell monolayers. The invention further allows for identifying endothelial cell receptors that bind the antibody thereby providing target receptors against which to isolate further cognate ligands and their associated transport systems and by which to identify transcytosis transporters targeted by the antibodies.

CROSS REFERENCE TO RELATED APPLICATION

This application is a continuation-in-part of U.S. application Ser. No. 11/759,723, filed Jun. 7, 2007, which claims the benefit of U.S. Provisional application 60/811,618, filed Jun. 7, 2006, both of which are incorporated herein by reference in their entirety for all purposes.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

This invention was made with United States government support awarded by the following agency: National Institutes of Health, Grant No. NS052649. The United States government has certain rights in this invention.

FIELD OF THE INVENTION

This invention relates generally to antibodies recognizing endothelial cell surface receptors and methods of identifying such antibodies.

BACKGROUND OF THE INVENTION

Treatment modalities for brain and neurological diseases are extremely limited due to the impermeability of the brain's blood vessels to most substances carried in the blood stream. The blood vessels of the brain, referred to collectively as the blood-brain barrier (BBB), are unique when compared to the blood vessels found in the periphery of the body. Tight apposition of BBB endothelial cells (EC) to neural cells like astrocytes, pericytes and neurons induces phenotypic features that contribute to the observed impermeability. Tight junctions between ECs comprising the BBB limit paracellular transport, while the lack of pinocytotic vesicles and fenestrae limit non-specific transcellular transport. These factors combine to restrict molecular flux from the blood to the brain to those molecules that are less than 500 daltons and also lipophilic. Thus, using the large mass transfer surface area (over 21 m² from 400 miles of capillaries in human brain) of the bloodstream as a delivery vehicle is largely infeasible except in those circumstances where a drug with the desired pharmacological properties fortuitously possesses the size and lipophilicity attributes allowing it to pass freely through the blood vessel. Because of such restrictions, it has been estimated that greater than 98% of all small molecule pharmaceuticals and nearly 100% of the emerging class of protein and gene therapeutics do not cross the BBB.

In addition to the physical barrier presented by the BBB, efflux transporters such as p-glycoprotein (MDR1) and members of the multi-drug resistance-associated protein family (MRP) serve to further limit brain uptake of even those small molecules that are small and lipophilic. FIG. 1A is a micrograph of a section of rat brain (V=ventricle) illustrating the sequestration of horseradish peroxidase in vessels, while in small brain regions perfused by capillaries lacking the BBB, the protein diffuses readily into brain tissue. FIG. 2A also illustrates the impermeable nature of the BBB: histamine (111 Da) remains sequestered within the blood vessels and does not enter the brain interior.

Although neurological diseases such as brain cancer, Alzheimer's disease, Parkinson's disease, and stroke continue to afflict people worldwide, there has been a paucity of new therapies to treat such diseases. Lack of treatment modalities can, in part, be attributed to the lack of effective brain delivery strategies. Due to this lack of treatment methods the National Institutes of Health tumor and stroke progress review groups have even identified the search for innovative strategies for drug or gene targeting through the blood-brain barrier as a top research priority. The National Institutes of Health (NIH) guidelines instruct that such breakthroughs in basic neuroscience can be delivered to the clinic and “require an agent delivery strategy and/or the ability to target specific areas of the brain”. Thus, in the absence of appropriate vehicles for targeting and trans-BBB transport, the pipeline of new CNS medicines will likely continue to be inadequate for the people suffering from neurological disorders. As examples, protein therapeutics known as neurotrophins have been investigated recently for their protective capacity in stroke, reversal of Parkinson's disease symptoms after direct infusion into the brains of human subjects, and for their ability to direct specialized differentiation of neural stem cells for potential treatment of Parkinson's disease and other neurodegenerative diseases such as Alzheimer's disease, Huntington's disease and multiple Sclerosis. Although extremely promising therapeutics, these trophic factors do not readily cross the BBB and will require a noninvasive delivery system for widespread, effective administration.

Present brain delivery strategies are particularly invasive and require circumvention of the BBB. Strategies requiring neurosurgery are used for implantation of polymer particles infused with drug, but the treatment volume is limited because the extracellular fluid in brain tissue is quiescent, and simple molecular diffusion only allows for a modest penetration distance of 2-3 mm. A similar method is direct injection of a drug into the brain ventricles, but the penetration into brain tissue is also limited for such intraventricular injections because the cerebral spinal fluid is rapidly cleared and is turned over 4-5 times daily. In addition, protein therapeutics, such as, for example, Glial-cell Line-Derived, Neurotrophic Factor (GDNF) for Parkinson's disease have been delivered through neurosurgically implanted catheters with continual drug infusion by a peripheral pump. Disruption of the BBB has been investigated using hyperosmolar solutions and vasoactive agents like serotonin and bradykinin peptides to allow free passage of molecules from the blood to the brain. This method is primarily used clinically only in terminal patients because alterations in the BBB can lead to toxic effects due to the free access of solutes and immune factors that are normally excluded from brain.

The aforementioned invasive strategies can have success for those diseases with limited treatment volumes, such as, for localized, non-metastatic brain tumors. However, for chronic conditions requiring a repetitive treatment regimen, or for those diseases present in large portions of the brain such as Alzheimer's disease, a noninvasive drug delivery strategy would be substantially more preferable and practical.

A variety of noninvasive brain drug delivery methods have been investigated that make use of the brain blood vessel network to gain widespread drug distribution. The brain capillary network has an average spacing of just 40 microns between capillaries and is sufficiently dense that each brain cell essentially has its own vessel for nutrient supply (FIG. 2). In addition, if the endothelial barrier of the BBB can be overcome such that a drug is deposited on the brain side of the BBB, the diffusion distance is short enough that each brain cell should be accessible to the drug. As a result, in contrast to invasive methods, a comprehensive treatment volume can result. These noninvasive transport systems/mechanisms can be generally clustered into three groups: 1, non-specific uptake; 2, carrier-mediated transport; and 3, receptor-mediated transport (FIG. 3).

Non-specific uptake mechanisms, while allowing some transport across the BBB, lack sensitivity and specificity. Cationic protein transduction domains fall into the realm of non-specific carriers, and although the HIV TAT peptide was shown to gain access to the brain interstitium after intraperitoneal injection, subsequent pharmacokinetic analysis indicated that the rapid clearance and broad organ uptake would necessitate very high doses to gain a pharmacologic effect. Another non-specific uptake mechanism is the surfactant coating of nanoparticles with polysorbate 80. Although the mechanism of brain uptake is still unresolved, the labile nature of the particles in vivo leads to short-lived pharmacologic effects and possible BBB permeabilization. Both of these non-specific methods suffer from a lack of selective targeting and result in widespread distribution of the active compound throughout the body with concomitant systemic effects.

Carrier-mediated drug transport relies on the presence of endogenous transmembrane proteins that are selective and stereospecific for small molecule solutes. For instance, L-dopa, administered to treat Parkinson's disease gains entry to the brain by utilizing the large amino acid transporter (LAT-1). The successful transport through the blood-brain barrier is a result of L-dopa mimicking the structure of phenylalanine with only the substitution of two hydroxyl groups on the aromatic ring of phenylalanine. Utilization of the saturable biotin transport system for delivery of biotinylated drugs has also been attempted. In addition, it is likely that the efflux of the AIDS drug AZT progresses in a carrier-mediated fashion. However, due to the stereospecificity and steric constraints imposed by these selective membrane pores, applications are potentially limited.

Receptor-mediated transport involves the binding of an exofacial epitope of a cell surface receptor and triggering of an energy intensive transcellular transport process known as transcytosis (FIG. 3). Drugs can be delivered using these portals if conjugated to the natural ligand or an antibody that can trigger the transcytosis process. This method has been successful in allowing for non-invasive transport of small molecules, proteins, genes, nanoparticles, and liposomes up to 100 nm in size. The receptors that are commonly targeted for transcytosis are the low density lipoprotein (LDL) receptor, the transferrin receptor, and the insulin receptor. Similar less specific processes involving absorptive-mediated transcytosis have been used with cationized proteins that promote receptor clustering and activation of the transcytosis pathway. Strategies oftentimes target the cell surface receptor in ways that do not disrupt the normal transport of endogenous ligand. Therefore the impact on normal metabolic pathways is limited. In addition, since transcytosis employs the vesicular trafficking system, this strategy is not nearly as limited by the size and shape constraints of carrier-mediated transport.

Antibodies are particularly well suited for targeting BBB receptor-mediated transcytosis systems given their high affinity and specificity for their ligands. As examples, appropriately-targeted antibodies that recognize extracellular epitopes of the insulin and transferrin receptors can act as artificial transporter substrates that are effectively transported across the BBB and deposited into the brain interstitium via the transendothelial route. Additionally, when conjugated to drugs or drug carriers of various size and composition, the BBB targeting antibodies mediate brain uptake of the therapeutic cargo. Noninvasive transport of small molecules such as methotrexate has been achieved using anti-transferrin receptor antibodies. Proteins such as nerve growth factor, brain derived neurotrophic factor, and basic fibroblast growth factor were delivered to the brain after intravenous administration by using an anti-transferrin receptor antibody. The latter two cases promoted reduction in stroke volume in rat middle cerebral artery occlusion models. Liposomes and liposomes containing genes have also been delivered to the brain in vivo using anti-transferrin receptor antibodies. In particular, gene-containing antibody-targeted liposomes have been targeted to rat brain for restoration of tyrosine hydroxylase activity in an experimental Parkinson's disease model and to primate brain using a humanized anti-insulin receptor antibody. In addition, brain delivery of the new class of RNA interference drugs via pegylated immunoliposomes has been demonstrated to increase survival of mice implanted with an experimental human brain tumor model. Further, anti-transferrin receptor conjugated nanoparticles have been produced. Finally, even if an antibody binds to the brain microvsculature or internalizes without full transcytosis, it can have drug delivery benefits. When conjugated to a liposome or nanoparticle loaded with lipophilic small molecule drugs, it might be possible to raise the local BBB concentration of drug and help circumvent brain efflux systems, thereby facilitating brain uptake. Finally, in the event binding occurs without transcytosis or even internalization, the identification of BBB-specific antibody receptors or ligands will further help to characterize and identify components of the transporter system and help to further optimize antibodies that do internalize and trancytose. Taken together, these results indicate the potential utility of antibody-targeted transcytosis systems for noninvasive trafficking of drugs into the brain.

Regardless of the promise shown for antibody mediated transport in prior studies, the current antibody targeting reagents lack specificity and transport efficiency. Although early results derived from the receptor-mediated transcytosis process are promising due to its robustness in delivery of drugs or drug carriers in many formats, it also has some serious drawbacks that need to be addressed for general clinical success. The present methods rely on receptors that are ubiquitously expressed like the transferrin and insulin receptors. This leads to mis-targeting of potentially expensive drugs that also may have unwanted side effects in tissues other than the brain. In addition, the present methodologies generally result in a low fraction (1-4%) of the injected dose actually reaching the brain target as a consequence of poor targeting and nonideal BBB permeability. This loss of between 96-99% of the administered therapeutic could hamper the development of these delivery approaches given the cost of drug manufacture, especially for protein and gene-based medicines that currently comprise nearly 700 drugs in various stages of clinical trials. Finally, the antibodies used in the aforementioned proof-of-concept experiments are either of murine origin or partially humanized, and this could lead to unwanted immunogenic reactions in human patients. Therefore, the identification of fully human antibodies that specifically recognize brain endothelial receptors would vastly improve the targeting and efficiency of drug delivery while minimizing side-effects.

SUMMARY OF THE INVENTION

This invention provides antibodies that bind endothelial cell receptors resulting in endocytosis of the receptor and bound ligands. In one exemplary embodiment, the invention comprises an isolated antibody fragment having the amino acid sequence set forth in any one of SEQ ID NOs:1-34. In another embodiment, the invention provides an isolated nucleic acid having a sequence coding for an amino acid as set forth in any one of SEQ ID NOs:1-34. In some preferred versions, the isolated antibody fragment is a single chain fragment variable (scFv) fragment. In other preferred versions, the isolated antibody is a Fab, an IgG or any other ligand specific to the endothelial cell receptor.

In another preferred embodiment, the invention is a pharmaceutical composition comprising an antibody linked to a pharmaceutically active compound that is useful in transferring the pharmaceutically active compound across the blood brain barrier (BBB).

In another exemplary embodiment, the invention is an isolated expression vector that includes a polynucleotide encoding the amino acid sequence set forth in SEQ ID NOs:1-34. In other embodiments, the invention includes a purified and isolated host cell comprising the expression vector containing the isolated nucleic acid encoding the amino acid sequence set forth in any one of SEQ ID NOs:1-34. It should be appreciated that the host cell can be any cell capable of expressing antibodies, such as, for example fungi, mammalian cells, including the Chinese hamster ovary cells; insect cells, using, for example, a baculovirus expression system; plant cells, such as, for example, corn, rice, Arabidopsis, and the like.

In yet another exemplary embodiment, the invention comprises a process for expressing an antibody fragment capable of binding to a brain endothelial cell receptor comprising: (a) displaying an antibody fragment on a yeast cell; (b) panning the antibody displaying yeast cell against a brain endothelial cell culture; (c) identifying displayed antibody fragments that specifically bind brain endothelial cell receptors; (d) inserting an isolated nucleic acid coding for the antibody fragment identified in step (c) in an expression vector; and (e) transforming a host cell with the expression vector. In some versions of this embodiment, the host cell is selected from the group consisting of: yeast, bacteria, and combinations thereof. In some preferred embodiments the host cell is Saccharomyces cerevisiae or E. coli.

In another exemplary embodiment, the invention is a method of identifying a brain endothelial cell specific antibody. This embodiment includes displaying antibody fragments on a yeast cell surface, panning the displayed antibody against a brain endothelial cell culture, isolating specific binders to the membrane receptors on the brain endothelial cell, and identifying the specific binders, thereby identifying an endothelial cell specific antibody. In some preferred embodiments the endothelial cell culture is provided in a cell monolayer.

In still another exemplary embodiment, the invention comprises a method of identifying endothelial cell receptors functioning in or related to endocytosis and transcytosis comprising, providing a cultured endothelial cell monolayer and panning a yeast-displayed antibody library against the endothelial cell monolayer, isolating antibody bound endothelial cells; and identifying the cognate receptor.

Novel human antibodies that target BBB transport systems have immense utility. Unlike the antibody delivery strategies that utilized well studied systems such as the transferrin and insulin systems, identifying novel receptor-mediated transport systems is quite difficult given that these ligands are membrane proteins that have yet to be identified. Therefore, the inventors have developed a novel selection methodology to identify fully human antibodies having the required functionality of BBB binding. The power of this technique is the concomitant selection of potential drug delivery vector and its cognate cell surface receptor (receptor-mediated carrier system) with no prior knowledge as to the origin of either component. FIG. 4 depicts a general scheme for the selection of such antibodies according to the invention.

Another aspect of the present invention is in regard to antibody targets at the blood brain barrier, particularly, targets that represent the molecular machinery for internalization (endocytosis) and transcytosis. Accordingly, the present invention is directed to a purified scFvA antigen having a molecular weight of approximately 124 kDa when immunoprecipitated by human scFvA under non-reducing conditions. The inventors identified and demonstrated this antigen is expressed in intact brain capillaries.

Accordingly, the invention further encompasses an antibody-blood brain barrier transporter system. Such a system includes: (a) an antigen having a molecular weight of approximately 124 kDa when immunoprecipitated by human scFvA under non-reducing conditions, the antigen expressed in intact brain capillaries; and (b) a purified antibody bound to the scFvA antigen. The purified antibody has the amino acid sequence set forth in any one of SEQ ID NOs:1-5, more preferably the antibody is scFvA having the amino acid sequence set forth in SEQ ID NO:1. In certain embodiments, the purified antibody is provided in combination with a pharmaceutically active compound.

As demonstration of a similar exemplary embodiment, the inventors have identified the scFvJ antibody's (SEQ ID NO:14) target antigen as neural cell adhesion molecule (NCAM). Thus, the invention further encompasses an antibody-blood brain barrier transporter system including (a) an antigen comprising NCAM; and (b) a purified antibody bound to the antigen. In certain embodiments, the purified antibody has the amino acid sequence set forth in SEQ ID NO:14. Preferably, the purified antibody is provided in combination with a pharmaceutically active compound.

Based upon the disclosed antibody-blood brain barrier transporter system, the invention also contemplates a method of delivering a pharmaceutically active compound across the blood brain barrier to a subject's brain. Such a method includes administering a pharmaceutically active compound in combination with a purified antibody having an amino acid sequence of any one of SEQ ID NOs:1-5, SEQ ID NOs:11-12, SEQ ID NO:15, and SEQ ID NO:21 to a subject such that the antibody directs delivery of the pharmaceutically active compound across the blood brain barrier to the subject's brain.

These and other features and advantages of various exemplary embodiments of the articles and methods according to this invention are described in, or are apparent from, the following detailed description of various exemplary embodiments of the methods according to this invention.

BRIEF DESCRIPTION OF THE DRAWINGS

Various exemplary embodiments of the methods of this invention will be described in detail, with reference to the following figures, wherein:

FIGS. 1A and 1B are micrographs illustrating the impermeability of the blood-brain barrier. FIG. 1A shows that horseradish peroxidase is sequestered in brain blood vessels and does not access the parenchyma, except for in the small circumventricular organs that lack a BBB (median eminence above). FIG. 1B. illustrates the effectiveness of the BBB: radio-labeled histamine, only 111 Da, cannot enter the brain or spinal cord of the mouse.

FIG. 2 is an electron micrograph of a human cerebellar cortex vascular cast illustrating the extent of the vascular network. Scale bar is 40 μm.

FIG. 3 is a schematic representation of various BBB transport options.

FIG. 4 is a flowchart of one embodiment of antibody-mediated brain endothelial cell transcytosis.

FIG. 5 is a cartoon of an immunoglobulin molecule illustrating the position of the variable regions and the origin of the single-chain antibody variable fragment (scFv). Variable light and heavy regions are connected by a flexible polypeptide linker and comprise the minimal binding subunit of an intact antibody.

FIGS. 6A-D are schematic representations of yeast surface display of an scFv construct (4-4-20) whose antigen is fluorescein. The scFv protein is fused to the self-assembling, mating agglutinin proteins (Aga1p and Aga2p) allowing surface display of scFv proteins that actively bind fluorescein on the surface of the yeast particle. FIG. 6A is a phase contrast image of yeast displaying 4-4-20. FIG. 6B is a fluorescence image of yeast displaying 4-4-20 bound to fluorescein-dextran (FITC-dextran). FIG. 6C is a phase contrast image of yeast displaying irrelevant scFv, D1.3. FIG. 6D is a fluorescence image of D1.3 yeast that fails to bind FITC-dextran.

FIG. 7 is a phase contrast image showing the specific interaction between yeast displaying 4-4-20 scFv and FITC-labeled RBE4 cells. Conjugation of 4-4-20 yeast cells with biotinylated and neutravidin-FITC (NAFITC) labeled (top row) or unlabeled (bottom row) RBE4 cells. Yeast and RBE4 cells can be distinguished by their size, 4 μm and 20 μm respectively. Images of the same microscope fields were taken before and after each washing step. Scale bar: 50 μm. As shown, the FITC labeled cells exhibit continued binding to yeast after 3 washes while the non-FITC labeled cells do not.

FIG. 8 is a bar graph showing the effects of scFv affinity on multiple round enrichment. Mixtures containing 4-4-20, 4M5.3 and D1.3 yeast (1:1:1×10⁵) were panned against NAFITC-labeled RBE4 cell monolayers. After each round, the fractions of 4-4-20 and 4M5.3 in the mixture were evaluated by flow cytometry. Solid bars correspond to 4-4-20 percentage and hatched bars correspond to 4M5.3 percentage. The dotted line indicates the detection limit of the flow cytometry assay.

FIG. 9 is a schematic representation illustrating the overall strategy of biopanning to identify BBB-binding and internalizing scFv.

FIG. 10 illustrates the enrichment of RBE4-binding scFv's via biopanning.

FIG. 11 is a schematic diagram of the cell monolayer panning and high throughput yeast clone profiling strategy. 11A, yeast growth in 96-well plate; 11B, yeast are added to RBE4 culture; 11C, induced yeast; 11D, non-induced; 11E initial PCR or binders; 11F Restriction digest providing “fingerprint” of binders and identifying germline family; 11G sequencing of unique scFv clones.

FIG. 12 is a table summarizing the binding of scFv variants. (a) Unique scFv were clustered by homology. Each class of scFv antibodies differs from all other classes by at minimum one CDR3 (20% amino acid homology). The CDR3 regions were focused upon for defining classes given the nonimmune basis for the library that limits CDR1 and CDR2 diversity and the fact that CDR3 of the VH and VL play a major role in determining binding specificity and affinity. Within a class, CDR1, CDR2, and CDR3 (≧85% amino acid homology) of VH and VL all have high homology. (b) An scFv was deemed unique by amino acid sequence and BstN1 digest pattern. (c) The germline antibody gene usage was determined by subjecting the deduced scFv amino acid sequence to IgBLAST (http://www.ncbi.nlm.hig.gov/igblast/). (d) Clones subtracted in the VHCDR2 yeast Northern blot experiments were counted in the totals of either scFvA or scFvD based on their frequency of occurrence in small scale screens, and therefore represent estimates.

FIG. 13 is a sequence alignment of scFv clones B, G, C and K that show sequence homology to clone scFv A. VH—variable heavy region; VL—variable light region; CDR—complimentarity determining region.

FIG. 14 is a sequence alignment of scFv clones D, I and H that share sequence homology. VH—variable heavy region; VL—variable light region; CDR—complimentarity determining region.

FIG. 15 is a sequence alignment of scFv clones A, C, B, G, K and F illustrating that F has a similar homology to the variable light (VL) domains but not to the variable heavy (VH) domain. VH—variable heavy region; VL—variable light region; CDR—complimentarity determining region.

FIG. 16 is a polyacrylamide gel (top panel) showing that the secreted proteins have the appropriate weight for an scFv and a table (bottom panel) summarizing the binding and internalization of scFv by RBE4 cells.

FIG. 17 is a collection of micrographs illustrating dual fluorescent staining of RBE4 binding scFv's showing specific binding and internalization of scFv A by RBE4 cells but not scFv D.

FIG. 18 provides equilibrium binding attributes of scFvA and scFvD. Left panel: binding isotherm for scFvA interaction with live RBE4 cells. The plot shows the fitted monomeric equilibrium binding functions and experimental data from two independent experiments. Right panel: binding isotherm for dimerized scFvD interaction with RBE4 cells. The plot shows the fitted monomeric equilibrium binding functions used to generate an apparent affinity (avidity) and experimental data from two independent experiments. Insets indicate raw flow cytometry histograms that were used to generate the binding curves.

FIG. 19 depicts yeast display immunoprecipitation of antigens for scFvA (A), scFvD (D), scFvJ (J) and OX26 scFv (O). Irrelevant anti-hen egg lysozyme scFv (N) was used as a negative control. The immunoprecipitation products were resolved by either nonreducing (NR) or reducing (R) gel electrophoresis and were probed with an anti-biotin antibody or an anti-transferrin receptor antibody (OX26).

FIG. 20 are fluorescence micrographs allowing evaluation of scFv binding and internalization properties. RBE4 cells were labeled with purified, pre-dimerized scFvA, scFvD, irrelevant scFv 4-4-20 or OX26 monoclonal antibody at 4° C. for cell surface labeling and then shifted to 37° C. to promote cellular trafficking. The cells were then labeled with AlexaFluor 555 conjugated anti-mouse IgG at 4° C. followed by AlexaFluor 488 conjugated anti-mouse IgG with or without cell permeabilization by saponin (SAP) treatment. Merged images of the AlexaFluor-labeled images are shown. Scale bar: 20 μm.

FIG. 21 are fluorescence micrographs showing that scFv A recognizes a brain endothelial antigen expressed in vivo. Frozen rat brain sections were co-labeled with scFvA (1) or 4-4-20 (4) and the brain endothelial cell marker GSA-FITC (2, 5). (3, 6) are merged images indicating the overlap between scFv and GSA-FITC labeling. In contrast to scFvA, irrelevant scFv 4-4-20 did not yield any labeling. Similar results were observed for mouse brain sections and freshly isolated capillaries. Finally, much like the ranking of antigen density for RBE4 cultures, qualitative labeling intensities indicated that the scFvA antigen density in vivo was higher than that for the transferrin receptor (data not shown). Scale bar: 50 μm.

FIG. 22 shows schematics of the relevant steps of the YDIP procedure. In step (1), target cells containing the antigen are lysed using detergents. Cell surface antigens such as membrane proteins are solubilized by the detergent. Yeast cells that have been induced for surface display of scFvs in step (2) are combined with the cell lysate from (1). In step (3), components in the cell lyste that are not bound to scFvs are washed away, and the yeast cells are collected by centrifugation. At this point, antibody-antigen characteristics can be quantified by flow cytometry (step 4). In step (5), denaturing conditions such as lowering the pH are used to dissociate the antigen-antibody interaction. The collected antigen can then be analyzed for antigen identification and characterization in step (6).

FIG. 23 shows ScFv binding activity in detergent solutions. (A) Equilibrium binding titration curves of yeast-displayed D1.3 scFv with HEL in PBS and containing the indicated detergents. The lines represent fitted solutions using least-squares regression with a standard bimolecular equilibrium binding model. BSA fixed indicates binding data using formaldehyde-fixed yeast. (B) Comparison of absolute levels of biotinylated HEL binding in various detergent solutions using unfixed (open bars) or formaldehyde-fixed (grey bars) yeast. HEL binding to D1.3 on the surface of yeast was detected by using a fluorescent streptavidin-phycoerythrin conjugate and quantitated by flow cytometry as the mean fluorescence (HEL binding) per cell. Data were normalized to the case of PBS-BSA. (C) Detection of antigen-antibody interaction for scFvA, scFvK, scFvD and scFvJ. Yeast cells displaying each scFv were labeled with biotinylated RBE4 cell lysate generated by 1% TX. Yeast displaying an irrelevant antibody were used as a negative control (NC). The inset shows an anti-biotin Western blot of antigens isolated using YDIP from biotinylated RBE4 cell lysate generated using OG. Lane 1: irrelevant scFv, lane 2: scFvA, lane 3: scFvK, lane 4: scFvD, and lane 5: scFvJ. (D) Measurement of relative affinities of scFvk by titrating RBE4 cell lysate generated with 1% OG. X-axis indicates the concentration of RBE4 lysate in terms of percent of a cell lysate containing approximately 2 mg of total protein. The light-chain CDR3 amino acid sequence of scFvA and scFvK and the relative affinity (K_(d)) calculated as described above are indicated in the inset. Error bars represent standard deviations from two (A and D) or three (B and C) independent measurements.

FIG. 24 shows recovered antigen purity and quantity by YDIP. (A) Comparison of elution methods from formaldehyde-fixed yeast cells displaying D1.3 scFv. The amount of biotinylated HEL recovered after each elution was quantified by Western blot. Elutions were performed using 3 M NaCl (High Salt), 0.2 M glycine-HCl pH 2.4 (Low pH), 0.2 M NaOH (High pH), 9 M urea (Urea), or 0.2% SDS in 0.1 M Tris (SDS). Elution with PBS-BSA was used as a negative control. The data represented mean±S.D. from triplicate measurements expressed as the percentage of maximum theoretical immunoprecipitation yield. (B) Yeast immunoprecipitation of HEL from RBE4 cell lysate with low pH elution. HEL was added to RBE4 cell lysates at a concentration of 34 nM and YDIP was performed. Immunoprecipitation products were separated using SDS-PAGE and subsequently silver-stained. YDIP was performed using either D1.3-displaying yeast (lanes 2 and 4) or an irrelevant 4420 scFv displaying yeast (lanes 1 and 3). Lanes 1 and 2 are YDIP products from unfixed yeast, and lanes 3 and 4 are from formaldehyde-fixed yeast. Lane 5 contains 25 ng of purified HEL for comparison. The gel was quantified by densitometric analysis.

FIG. 25 shows serial elution method of antigen concentration. (A) The scFvJ antigen was immunoprecipitated from biotinylated RBE4 cell lysate using fixed yeast. Elution was performed by adding 50 μL of 0.2 M glycine-HCl buffer (pH 2.0) to serially elute batches of 6×10⁷ immunoprecipitated yeast. Each lane number corresponds to the number of yeast batches eluted. (B) Densitometric quantitation of (A).

FIG. 26 shows VDIP coupled with MS/MS for antigen identification. (A) Silver-stained gel showing the scFvJ YDIP product separated by SDS-PAGE. Lane 1: raw cell lysate, Lane 2: YDIP using yeast displaying irrelevant scFv, Lane 3: YDIP using yeast displaying scFvJ. Although coomassie-stained gels were used for MS/MS experiments, a silver-stained gel is shown for clarity. The scFvJ antigen band that corresponds to the band identified by anti-biotin Western blotting is indicated by an arrowhead. (B) MS/MS results showing the two peptides sequenced that correspond to NCAM. All the y-ions identified are indicated on the figure along with the m/z values. The Mascot score of each ion is also indicated and as defined in Table 2, the NCAM identification has a confidence level of p<0.05. (C) Confirmation of antigen identification by Western blotting. The left panel (lanes 1-3) was probed with an anti-biotin antibody and the right panel (lanes 4-6) was probed with an anti-NCAM antibody. Lanes 1 and 4: raw biotinylated RBE4 cell lysate, lanes 2 and 5: VDIP product from irrelevant scFv, lanes 3 and 6: VDIP product from scFvJ.

DETAILED DESCRIPTION OF THE INVENTION

The current invention is based on the observation that cellular mechanisms may be the most efficient and effective way to transport drugs and/or therapeutics across the blood brain barrier (BBB). While a variety of cellular transporter and receptor mechanisms have been identified, they are limited by the specificity of the ligand to the endothelial receptor and by both the affinity and avidity of the ligand for the receptor. Further, identification of, as yet, unidentified antibody ligands and receptors will provide better tools by which to transport compounds across the BBB.

The inventors have mined a human single-chain antibody fragment (scFv) library for scFvs that bind to membranes of brain endothelial cells. A subset of the scFv identified as binding to brain endothelial cells also endocytose into these cells, indicating that they may be substrates for BBB transcytosis systems. The scFv also specifically labels vessels of all sizes in brain tissue sections in a pattern that represents a transport system of endothelial origin. No labeling is detected in other brain cells. This class of scFv and their associated BBB transport systems represent a novel mechanism for noninvasive drug delivery to the brain.

Before the present invention is described, it is understood that this invention is not limited to the particular methodology, protocols, and reagents described, as these may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention which will be limited only by the appended claims.

It must be noted that as used herein and in the appended claims, the singular forms “a”, “an”, and “the” include plural reference unless the context clearly dictates otherwise. Thus, for example, reference to “a cell” includes a plurality of such cells and equivalents thereof known to those skilled in the art, and so forth. As well, the terms “a” (or “an”), “one or more” and “at least one” can be used interchangeably herein. It is also to be noted that the terms “comprising”, “including”, and “having” can be used interchangeably.

Unless defined otherwise, all technical and scientific terms used herein have the same meanings as commonly understood by one of ordinary skill in the art to which this invention belongs. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. All publications mentioned herein are incorporated herein by reference for the purpose of describing and disclosing the chemicals, cell lines, vectors, animals, instruments, statistical analysis and methodologies which are reported in the publications which might be used in connection with the invention. Nothing herein is to be construed as an admission that the invention is not entitled to antedate such disclosure by virtue of prior invention.

As used herein “subject” means mammals and non-mammals. “Mammals” means any member of the class Mammalia including, but not limited to, humans, non-human primates such as chimpanzees and other apes and monkey species; farm animals such as cattle, horses, sheep, goats, and swine; domestic animals such as rabbits, dogs, and cats; laboratory animals including rodents, such as rats, mice, and guinea pigs; and the like. Examples of non-mammals include, but are not limited to, birds, and the like. The term “subject” does not denote a particular age or sex.

As used herein, “administering” or “administration” includes any means for introducing compositions of the invention into the body, preferably into the systemic circulation. Examples include but are not limited to oral; buccal, sublingual, pulmonary, transdermal, transmucosal, as well as subcutaneous, intraperitoneal, intravenous, and intramuscular injection.

As used herein, “pharmaceutical composition” means therapeutically effective amounts of the BBB transcytosis compound (also termed “pharmaceutically active compound”) together with suitable diluents, preservatives, solubilizers, emulsifiers, and adjuvants, collectively “pharmaceutically-acceptable carriers.” As used herein, the terms “effective amount” and “therapeutically effective amount” refer to the quantity of active therapeutic agent or agents sufficient to yield a desired therapeutic response without undue adverse side effects such as toxicity, irritation, or allergic response. The specific “effective amount” will, obviously, vary with such factors as the particular condition being treated, the physical condition of the subject, the type of animal being treated, the duration of the treatment, the nature of concurrent therapy (if any), and the specific formulations employed and the structure of the compounds or its derivatives. In this case, an amount would be deemed therapeutically effective if it resulted in one or more of the following: (a) the prevention of a neurological or brain disease (e.g., Alzheimers, Parkinson's and/or cancer); and (b) the reversal or stabilization of a neurological or brain disease (e.g., Alzheimers, Parkinson's and/or cancer). The optimum effective amounts can be readily determined by one of ordinary skill in the art using routine experimentation.

Pharmaceutical compositions are liquids or lyophilized or otherwise dried formulations and include diluents of various buffer content (e.g., Tris-HCl, acetate, phosphate), pH and ionic strength, additives such as albumin or gelatin to prevent absorption to surfaces, detergents (e.g., Tween 20, Tween 80, Pluronic F68, bile acid salts), solubilizing agents (e.g., glycerol, polyethylene glycerol), anti-oxidants (e.g., ascorbic acid, sodium metabisulfite), preservatives (e.g., Thimerosal, benzyl alcohol, parabens), bulking substances or tonicity modifiers (e.g., lactose, mannitol), covalent attachment of polymers such as polyethylene glycol to the protein, complexation with metal ions, or incorporation of the material into or onto particulate preparations of polymeric compounds such as polylactic acid, polyglycolic acid, hydrogels, etc, or onto liposomes, microemulsions, micelles, milamellar or multilamellar vesicles, erythrocyte ghosts, or spheroplasts. Such compositions will influence the physical state, solubility, stability, rate of in vivo release, and rate of in vivo clearance. Controlled or sustained release compositions include formulation in lipophilic depots (e.g., fatty acids, waxes, oils).

Further, as used herein “pharmaceutically acceptable carriers” are well known to those skilled in the art and include, but are not limited to, 0.01-0.1M and preferably 0.05M phosphate buffer or 0.9% saline. Additionally, such pharmaceutically acceptable carriers may be aqueous or non-aqueous solutions, suspensions, and emulsions. Examples of non-aqueous solvents are propylene glycol, polyethylene glycol, vegetable oils such as olive oil, and injectable organic esters such as ethyl oleate. Aqueous carriers include water, alcoholic/aqueous solutions, emulsions or suspensions, including saline and buffered media.

For purposes of the present invention, “treating” or “treatment” describes the management and care of a subject for the purpose of combating the disease, condition, or disorder. The terms embrace both preventive, i.e., prophylactic, and palliative treatment as well as therapeutic treatment. Treating includes the administration of a compound of present invention to prevent the onset of the symptoms or complications, alleviating the symptoms or complications, or eliminating the disease, condition, or disorder.

In one exemplary embodiment, the invention comprises an isolated antibody fragment having the amino acid sequence set forth in any one of SEQ ID NOs:1-34. In some preferred versions, the isolated antibody fragment is a single chain fragment variable (scFv) fragment.

In another exemplary embodiment, the invention provides antibodies that bind endothelial cell receptors resulting in endocytosis of the receptor and bound ligands. In some embodiments, the invention is a pharmaceutical composition comprising an antibody linked to a pharmaceutically active compound that is useful in transferring the pharmaceutically active compound across the blood brain barrier (BBB).

In another exemplary embodiment, the invention is an expression vector that includes a polynucleotide encoding the amino acid sequence set forth in any one of SEQ ID NOs:1-34. In other embodiments, the invention includes a purified and isolated host cell comprising the expression vector containing the isolated nucleic acid encoding the amino acid sequence set forth in any one of SEQ ID NOs:1-34. It should be appreciated that the host cell can be any cell capable of expressing antibodies, such as, for example fungi, mammalian cells, including the Chinese hamster ovary cells; insect cells, using, for example, a baculovirus expression system; plant cells, such as, for example, corn, rice, Arabidopsis, and the like. See, generally, Verma, R. et al., J Immunol Methods. 1998 Jul. 1; 216(1-2):165-81.

In yet another exemplary embodiment, the invention comprises a process for expressing an antibody fragment capable of binding to a brain endothelial cell receptor comprising: (a) displaying an antibody fragment on a yeast cell; (b) panning the antibody-displaying yeast cell against a brain endothelial cell culture; (c) identifying displayed antibody fragments that specifically bind brain endothelial cell receptors; (d) inserting an isolated nucleic acid coding for the antibody fragment identified in (c) in an expression vector; and (e) transforming a host cell with the expression vector. In some versions of this embodiment, the host cell is selected from the group consisting of: yeast, bacteria, and combinations thereof. In some preferred embodiments the host cell is Saccharomyces cerevisiae or E. coli.

In another exemplary embodiment, the invention is a method of identifying a brain endothelial cell specific antibody. This embodiment includes displaying antibody fragments on a yeast cell surface, panning the displayed antibody against a brain endothelial cell culture, isolating specific binders to the membrane receptors on the brain endothelial cell, and identifying the specific binders, thereby identifying an endothelial cell specific antibody. In some preferred embodiments the endothelial cell culture is provided in a cell monolayer.

In still another exemplary embodiment, the invention comprises a method of identifying endothelial cell receptors functioning in or related to endocytosis and transcytosis comprising, providing a cultured endothelial cell monolayer and panning a yeast-displayed antibody library against the endothelial cell monolayer, isolating antibody bound endothelial cells; and identifying the cognate receptor.

Novel human antibodies that target BBB transport systems have immense utility. Unlike the antibody delivery strategies that utilized well studied systems such as the transferrin and insulin systems, identifying novel receptor-mediated transport systems is quite difficult given that these ligands are membrane proteins that have yet to be identified. Therefore, the inventors have developed a novel selection methodology to identify fully human antibodies having the required functionality of BBB binding. The power of this technique is the concomitant selection of potential drug delivery vector and its cognate cell surface receptor (receptor-mediated carrier system) with no prior knowledge as to the identity of either component. FIG. 4 depicts a general scheme for the selection of such antibodies according to the invention.

If antibodies are used to target receptor-mediated transport systems at the BBB, then drug molecules and drug carriers can be effectively transcytosed across the BBB endothelium into brain tissue. Such noninvasive delivery from blood to brain is a result of the antibody acting as a surrogate ligand for the endogenous transport systems. Current known antibody-targeted brain delivery systems include the transferrin and insulin receptor systems. These receptors are expressed ubiquitously throughout the body and lead to mistargeting of expensive pharmaceuticals.

Depending on the neuronal disorder targeted, a variety of brain drug cargoes, e.g. pharmacologic compounds or, equivalently, pharmaceutically active compounds, can be delivered successfully in vivo using antibody-based targeting according to the invention. As used herein, the terms “pharmaceutically active compound” and “pharmacologic compound” shall refer to any compound useful in treating or ameliorating the effects of a disease or disorder. For example, diseases including neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, amyotrohpic lateral sclerosis (ALS, Lou Gehrig's disease) and multiple sclerosis can be targeted by use of such drugs as neurotrophic factors, including, but not limited to, nerve growth factor (NGF), brain derived neurotrophic factor (BDNF), ciliary neruotrophic factor (CNTF), glial cell-line neurotrohphic factor (GDNF) and insulin-like growth factor (IGF). In addition, other compounds that have been shown to have therapeutic potential and may be delivered by antibodies of the invention are neuropeptides, including, but not limited to, Substance P, neuropeptide Y, vasoactive intestinal peptide (VIP), gamma-amino-butyric acid (GABA), dopamine, cholecystokinin (CCK), endorphins, enkephalins and thyrotropin releasing hormone (TRH). Further, therapeutics may include cytokines, anxiolytic agents, anticonvulsants, polynucleotides and transgenes, including, for example, small-interfering RNAs which may be used for such neuronal disorders, including, but not limited to, psychiatric illnesses, such as, for example anxiety, depression, schizophrenia, and sleep disorders, as well as epilepsies, seizure disorders, stroke and cerebrovascular disorders, encephalitis and meningitis, memory and cognition disorders, pain therapeutics and physical trauma.

Antibodies are particularly well suited for targeting BBB receptor-mediated transcytosis systems given their high affinity and specificity for their ligands. As examples, appropriately-targeted antibodies that recognize extracellular epitopes of the insulin and transferrin receptors can act as artificial transporter substrates that are effectively transported across the BBB and deposited into the brain interstitium via the transendothelial route. Additionally, when conjugated to drugs or drug carriers of various size and composition, the BBB targeting antibodies mediate brain uptake of the therapeutic cargo. Noninvasive transport of small molecules such as methotrexate has been achieved using anti-transferrin receptor antibodies. Proteins such as nerve growth factor, brain derived neurotrophic factor, and basic fibroblast growth factor were delivered to the brain after intravenous administration by using an anti-transferrin receptor antibody. The latter two cases promoted reduction in stroke volume in rat middle cerebral artery occlusion models. Liposomes and liposomes containing genes have also been delivered to the brain in vivo using anti-transferrin receptor antibodies. In particular, gene-containing antibody-targeted liposomes have been targeted to rat brain for restoration of tyrosine hydroxylase activity in an experimental Parkinson's disease model and to primate brain using a humanized anti-insulin receptor antibody. In addition, brain delivery of the new class of RNA interference drugs via pegylated immunoliposomes has been demonstrated to increase survival of mice implanted with an experimental human brain tumor model. In addition, anti-transferrin receptor conjugated nanoparticles have been produced. Finally, even if an antibody binds to the brain microvasculature or internalizes without full transcytosis, it can have drug delivery benefits. When conjugated to a liposome or nanoparticle loaded with lipophilic small molecule drugs, it might be possible to raise the local BBB concentration of drug and help circumvent brain efflux systems, therefore facilitating brain uptake. Further, the ability to bind without internalization or with internalization but without full trancytosis will provide for the identification of BBB endothelial receptors or ligands that, once known, will allow for characterization and identification of the transporter system and for optimization of antibodies that are internalized and/or trancytosed. Taken together, these results indicate the utility of antibody-targeted transcytosis systems for noninvasive trafficking of drugs into the brain.

As can be appreciated, one aspect of the present invention is in regard to antibody targets at the blood brain barrier, particularly, targets that represent the molecular machinery for internalization (endocytosis) and transcytosis. Accordingly, the present invention is directed to a purified antigen having a molecular weight of approximately 124 kDa when immunoprecipitated by human scFvA under non-reducing conditions. The inventors identified and demonstrated this antigen is expressed in intact brain capillaries. The inventors have further demonstrated that scFvB, scFvC, scFvG, and scFvK each recognize and are capable of immunoprecipitating the approximately 124 kDa antigen immunoprecipitated by scFvA. Accordingly, scFvA, scFvB, scFvC, scFvG, and scFvK (SEQ ID NOs:1-5, respectively) are each useful as inventive blood brain targeting antibodies.

Accordingly, the invention further encompasses an antibody-blood brain barrier transporter system. Such a system includes: (a) an antigen having a molecular weight of approximately 124 kDa when immunoprecipitated by human scFvA under non-reducing conditions, the antigen expressed in intact brain capillaries; and (b) a purified antibody bound to the antigen wherein said antibody has the amino acid sequence set forth in any one of SEQ ID NOs:1-5. The purified antibody is preferably an scFvA antibody (SEQ ID NO:1), and, even more preferably, the scFvA antibody is provided in combination with a pharmaceutically active compound.

Furthermore, the inventors have identified neural cell adhesion molecule (NCAM) as an antigen that is immunoprecipitated by scFvJ antibody (SEQ ID NO:14). Accordingly, the invention further encompasses an antibody-blood brain barrier transporter system including: (a) an antigen comprising neural cell adhesion molecule (NCAM); and (b) a purified antibody bound to the antigen. In such a transporter system, the purified antibody binds to the NCAM antigen in the cell surface and is transported through the blood-brain barrier. In certain embodiments, the antibody included in the transporter system has the amino acid sequence set forth in SEQ ID NO:14. Preferably, the purified antibody is provided in combination with a pharmaceutically active compound, and the transporter system acts to facilitate the transfer of the pharmaceutically active compound across the blood-brain barrier.

Based upon the disclosed antibody-blood brain barrier transporter system, the invention also contemplates a method of delivering a pharmaceutically active compound across the blood brain barrier to a subject's brain. Such a method includes administering a pharmaceutically active compound in combination with a purified antibody having an amino acid sequence set forth in any one of SEQ ID NOs:1-5, SEQ ID NOs:11-12, SEQ ID NO:15, and SEQ ID NO:21 to a subject such that the antibody directs delivery of the pharmaceutically active compound across the blood brain barrier to the subject's brain. The purified antibody is preferably an scFv antibody having the amino acid sequence set forth in any one of SEQ ID NOs:1-5, SEQ ID NO:11, SEQ ID NO:15, and SEQ ID NO:21, and the purified antibody is more preferably an scFvA antibody having the amino acid sequence set forth in SEQ ID NO:1.

In general, methods of conjugating, linking and coupling antibodies to pharmacologically active compounds are well known in the field. For example, see, Wu A M, Senter P D, Arming antibodies: prospects and challenges for immunoconjugates, Nat. Biotechnol. 2005 September; 23(9):1137-46 and Trail P A, King H D, Dubowchik G M, Monoclonal antibody drug immunoconjugates for targeted treatment of cancer, Cancer Immunol Immunother. 2003 May; 52(5):328-37; Saito G, Swanson J A, Lee K D. Drug delivery strategy utilizing conjugation via reversible disulfide linkages: role and site of cellular reducing activities, Adv Drug Deliv Rev. 2003 Feb. 10; 55(2):199-215. As well, the present antibodies may be provided in combination with liposome, nanoparticles or other analogous carriers loaded with a pharmaceutically active compound. Methods of preparing such compositions are known in the field (see, for example, Sugano et al., Antibody Targeting of Doxorubicin-loaded Liposomes Suppresses the Growth and Metastatic Spread of Established Human Lung Tumor Xenografts in Severe Combined Immunodeficient Mice Cancer Research 60, 6942-6949, Dec. 15, 2000 and Martin et al., Nanomaterials in Analytical Chemistry, Analytical Chemistry News & Features, May 1, 1998; pp. 322 A-327 A). As used herein, the phrase “antibody in combination with a pharmaceutically active compound” shall not be limited by the method of manufacture and such compositions may be produced by, but not limited to, techniques of conjugating, linking, coupling and decorating known in the art.

The examples described below disclose antibody delivery vectors that are a critical component for disease-based applications. Identification of such vectors combines an innovative combinatorial antibody screening technology with expertise in the BBB and brain drug delivery fields to attack a complex delivery problem.

EXAMPLES

Various exemplary embodiments of compounds obtained as generally described above and methods according to this invention will be understood more readily by reference to the following examples, which are provided by way of illustration and are not intended to be limiting of the invention in any fashion.

Example 1 In Vitro Profiling of Brain Endothelial Cell Surface Using Large scFv Libraries

In order to simultaneously identify both brain endothelial cell surface proteins (potential BBB-resident transport systems) and antibody targeting reagents (drug delivery vector), the inventors have performed validation of a novel cell surface profiling or “panning” technique. This technique uses a combinatorial library of naïve single-chain antibodies (scFv, FIG. 5) displayed on the surface of yeast to probe the surface of endothelial cells. The antibody library contains ˜10⁹ different scFv, and this diverse collection can be thought of as an “in vitro immune system”. In this context, antibody-cell surface antigen pairs can be identified in a high throughput fashion. Yeast surface display has been well established as a technology for the directed evolution of antibody and T-cell receptors. The display system involves tethering single-chain antibodies to endogenous yeast mating agglutinins via a polypeptide linker (FIG. 6). This platform results in the display of 10⁴-10⁵ copies of a given scFv on the yeast cell surface where it is in prime position to sample the extracellular environment. Once a single yeast clone is isolated from a library of antibodies, it acts as a “monoclonal” scFv producer. For the profiling of the endothelial cell surface targeting efficacy, experiments were performed on model ligand systems confirming that it is possible to perform yeast cell-endothelial cell screens. Similar screens were then performed to identify scFvs recognizing endocytosing brain endothelial cell surface constituents.

Example 2 Yeast Cell-Endothelial Cell Targeting with a Model Ligand

The effectiveness of the panning method was first investigated using a model scFv-surface ligand system (Wang, X. X. and Shusta, E. V. The use of scFv-displaying yeast in mammalian cell surface selections. J Immunol Methods 2005, 304, 30-42) (incorporated herein in its entirety for all purposes). Briefly, the hapten fluorescein was used as the surface ligand and an anti-fluorescein scFv (4-4-20) was used as the yeast-displayed antibody. This system allowed detailed investigation of the factors governing panning success. Yeast displaying 4-4-20 exhibited specific interactions with fluoresceinated rat brain endothelial cells (RBE4 cell line Roux, F., et al., Regulation of gamma-glutamyl transpeptidase and alkaline phosphatase activities in immortalized rat brain microvessel endothelial cells. J Cell Physiol 1994, 159, 101-13.) (FIG. 7) and could be recovered from large backgrounds of nonbinding irrelevant yeast (1 in 10⁶) in just three rounds. These high efficiency selections required as few as 1700 fluorescein ligands per cell indicating the sensitivity and applicability to low abundance membrane proteins (transporters). Addition of free fluorescein competitor was able to completely ablate the yeast-EC interactions, confirming the specificity of the interaction.

The effects of scFv affinity on conjugate formation were examined since the naïve yeast library contains antibodies with affinities in the nanomolar range. The extent of enrichment was analyzed for dilute mixtures containing both 4-42-0 (Kd=1.3 nM) and a high affinity mutant 4M5.3 (Kd=270 fM) [55] at varying cell surface FITC intensities. Briefly, 4-4-20:4 M5.3:nonbinder mixtures of 1:1:10⁵ were applied to NAFITC-labeled monolayers having varying densities of fluorescein ligand. After a two hour incubation at 4° C., the wells were washed to remove non-specific binders. The simultaneous enrichment of 4-4-20 and 4M5.3 was analyzed over three consecutive enrichment rounds (FIG. 7). At 1,700 ligands per cell, both scFvs enriched with nearly equal efficiencies, while at the intermediate ligand densities, the 4M5.3 enriched more rapidly. In these cases, the final product after three rounds contained between 15-25% 4-4-20 with the balance being the higher affinity 4M5.3 scFv (FIG. 8). This result shows that it is possible to extract multiple scFv clones against a single cell surface target and also suggests that scFvs against multiple antigens can be simultaneously enriched using this method. Therefore, the next step was to complete a panning selection against true endothelial antigens. An initial strategy for cell culture panning of a yeast display library was developed as shown in FIG. 9.

Example 3 Overall Strategy for Identification of Blood Brain Barrier Binding and Internalizing scFv

Recognizing the limitations of phage-display, the strategy illustrated in FIG. 9 was developed as a more powerful assay for the identification of scFv's that bind brain endothelial cells. Briefly, as schematically represented in FIG. 9, the scFv library was mixed with an in vitro culture of brain endothelial cells. If a yeast cell has an antibody against a surface protein on endothelial cells, the yeast cell can bind to endothelial cells under proper conditions. If the surface protein is at a higher level, the binding may be more robust. This allowed the yeast binders to be recovered to perform further binding and purification. Specific binders were subjected to functionality tests to determine if they can be endocytosed and trancytosed by endothelial cells and to further identify brain-epitope specificity. This is the first example of yeast-display antibody screening on whole cells. There are numerous advantages to performing antibody screening using yeast-display (YSD) instead of phage-display. YSD has a very low background binding, due to the flocculin-deficient strain of yeast expressing the scFv library; in contrast, phage particles tend to nonspecifically bind to mammalian target cells thereby giving false-positive binders. In addition the low background in YSD increases the signal to noise ratio thereby leading to fast enrichment of binding clones and also the ability to identify clones that bind with low affinity Yeast express from 50,000 to 100,000 scFv on their surface while phage display antibody libraries express only 0-5 Ab/phage. This large number of expressed surface scFv's allows for further identification of weak binders due to the avidity effect which could cause strong cumulative interactions between relatively low affinity Abs and their antigens. Further, scFv displayed on yeast surface can be easily produced as a soluble protein by shuttling the scFv expression cassette into a secretion-expression vector. Thus, internalization studies of the scFv can be performed.

Example 4 Successful Screening of Human Nonimmune scFv Library for Brain Endothelial Cell Binding Clones

The inventors possess a human nonimmune scFv library in the identical yeast display format as that used for the studies described in Example 1. Methods of making such a library are known in the art and have been described by, e.g., Feldhaus et al. at Nat. Biotechnol. 21(2):163-70 (2003), incorporated by reference herein. The library is comprised of ˜1×10⁹ scFvs that represent much of the in vivo human antibody heavy and light chain gene diversity. Since the library is naïve, it has not been subjected to any prescreening against antigen and thus can provide antibodies that bind a widely diverse range of antigens. The library has been successfully used to isolate panels of scFvs that bind with high affinity (K_(d)=1-1000 nM) to hapten antigens (fluorescein), peptide antigens having different phosphorylation states (p53), protein antigens (lysozyme), and the extracellular portion of cell surface receptors (epidermal growth factor receptor). The yeast-EC targeting method described in Example I was used for the profiling of RBE4 rat brain endothelial cells using the scFv library. Briefly, the yeast library was applied to 100 cm² of RBE4 cells, and the binding yeast clones recovered and amplified (FIG. 9). This process was repeated for three more rounds on 20, 10, and 10 cm² of RBE4 cells, respectively. The surface area of endothelial cells required decreases progressively with each round since the diversity of the library decreases. Thus, fewer yeast clones need to be examined to exhaustively cover the enriched pools. After just four rounds of selection, the number of recovered yeast was nearly equal to the number of yeast applied to the RBE4 cells indicating that almost the entire pool was comprised of endothelial cell binding yeast clones (FIG. 10). Next, the individual clones from the recovered yeast pool were analyzed on a high throughput basis to determine the identity of the scFvs mediating yeast-RBE4 cell binding.

Example 5 Efficacy of Identification and Enrichment of RBE4-Binding scFv's Via Biopanning

The inventors developed the biopanning antibody library screening method based on the model system described in EXAMPLE 2. This model was then applied to the YSD scFv library to identify BBB-binding and internalizing antibodies. Preparation of the library is described by Wang et al. at Nat. Methods, 4(2):143-5 (2007) which, along with the references cited therein, is incorporated by reference into the present disclosure. FIG. 10 illustrates the effects of multiple rounds of enrichment using this method. As shown, after 4 rounds of panning, there were a lot of yeast cells retained by the RBE4 cells compared to after the third round. Further, almost all of the input yeast population was recovered after the fifth round indicating that four rounds of screening is apparently enough to “pull out” the BBB binders and the presubtraction experiments against other cell types or endothelium could be used to screen for brain specificity. The recovery percentage of the library is listed in the table in the lower panel of FIG. 10. The efficacy of the method is illustrated by the increasing recovery percentage of the library after progressive panning rounds. In comparison, the values for the negative control 4-4-20 yeast stayed the same.

Example 6 High Throughput Analysis of RBE4 Binding Competent Yeast Clones

While the capability of the inventors' panning system was illustrated by the results shown in FIG. 10, the inventors still needed a method by which to rapidly review the clones in the library. Therefore, the inventors developed a method to allow the high-throughput screening and sequencing of binding clones. Briefly, yeast clones were grown in a 96-well format such that scFv expression was induced on their surface (FIG. 11A). The yeast were then transferred directly to a 96-well plate containing RBE4 cell monolayers (FIG. 11B). Subsequent to appropriate washing, the 96-well plate was scanned by light microscopy. Yeast clones that truly mediate binding are simply identified by the retention of yeast on the RBE4 cell monolayer (FIG. 11C). To ensure that endothelial cell binding is not simply a result of a spurious genetic mutation in the yeast strain, a parallel plate was tested using yeast grown in a carbon source that does not allow induction of scFv expression (FIG. 11D). After incubation and washing steps, the induced binder clones (FIG. 11C) had many yeast left but there were relatively few for the noninduced yeast (FIG. 11D). The nonbinder clones had few yeast left for both induced and noninduced groups. No yeast mutants were identified in this particular screen and all binding was scFv mediated. Once the yeast binders were identified, colony PCR was performed to amplify the open reading frame of each scFv clone (FIG. 11E). Briefly, the scFv-encoding plasmid was amplified directly from the yeast cells using restriction enzyme BstNI. This enzyme cuts DNA frequently so different DNA would show different digestion patterns or fingerprints (FIG. 11F). Unique scFv clones will generally exhibit a different restriction profile due to the frequent occurrences of the five nucleotide BstNI recognition site. ScFvs having unique BstNI digestions were subject to sequencing. The PCR product of each clone exhibiting a unique restriction pattern was directly sequenced and the germline origin identified by IgGBLAST (FIG. 11G). A summary of unique clones is provided in the table shown in FIG. 12.

Example 7 Summary of Binding scFv Variants

FIG. 12 is a table summarizing binding of scFv variants. As shown, to date, a total of 2000 clones have been screened. Of the 2000 clones, 1760 bound RBE4 cells. The binding clones are listed in FIG. 12. The clones are organized such that the scFv's of the same germline usages are clustered together. scFv's in each subset share high sequence homology. However, regardless of the homology, CDRs varying in only 1 amino acid may bind different antigens and thus, each may be unique binders. Further, even if the clones bound the same antigen they may bind with different affinity. In addition, it should be noted that some of the scFv's appear only once among all the clones screened. This illustrates the power of the high throughput screening method developed as such rare binders would otherwise not have been detected.

Example 8 Identification of scFv Germline Family

The germline family usages of these clones are summarized in FIG. 12. Unique scFv were clustered by homology. Each class of scFv antibodies differs from all other classes by at minimum one CDR3 (<20% amino acid homology). The CDR3 regions were focused upon for defining classes given the nonimmune basis for the library that limits CDR1 and CDR2 diversity and the fact that CDR3 of the VH and VL play a major role in determining binding specificity and affinity. Within a class, CDR1, CDR2 and CDR3 (>85% amino acid homology) of VH and VL all have high homology. FIG. 12 also shows that scFv A and D dominate in the analyzed clones. This would prevent the analysis of more clones so the inventors developed an in situ Northern blotting method to first identify scFv A and D and then analyze non-A or D clones using the high-throughput method.

A total of approximately 2000 clones from the fourth round of panning have been analyzed using this method. Of the 34 unique scFvs identified thus far, only a few clones were recovered multiple times, and based on statistical considerations, many unique clones remain in the enriched round 4 pool. The germline origins of the heavy and light variable regions for the recovered clones are indicated in FIG. 12 and two clones (E and J) consist only of the heavy chain variable region. The complete method allows for rapid analysis of 1000's of BBB binding scFv clones. A sequence alignment of the scFv A-like clones is given in FIG. 13, an alignment of the scFv D-like clones is given in FIG. 14 and an alignment of F with the A-like clones is given in FIG. 15.

Example 9 Binding and Internalization of scFv by RBE4

While the test for efficacy of the yeast library began with an identification of the binding clones, their use in transcytosis further requires that the scFvs could be internalized. Therefore, the scFv's were also examined to see if they could be internalized by RBE4 cells. Because yeast are too big to be internalized the scFv was produced as a soluble protein in yeast cell culture. To do this, scFv gene in the YSD plasmid was subcloned into a secretion plasmid (described below in EXAMPLE 10) and the scFv was then secreted into the yeast cell culture medium. Briefly, the scFv open reading frames for several of the scFvs in FIG. 12 were subcloned into a yeast expression system that yields mg/L levels of active, purified scFv (Shusta, E. V., et al., Directed evolution of a stable scaffold for T-cell receptor engineering. Nat Biotechnol 2000, 18, 754-9; Shusta, E. V., et al., Increasing the secretory capacity of Saccharomyces cerevisiae for production of single-chain antibody fragments. Nat Biotechnol 1998, 16, 773-7; Shusta, E. V., et al., Yeast polypeptide fusion surface display levels predict thermal stability and soluble secretion efficiency. J Mol Biol 1999, 292, 949-56). This system is regulated by the galactose-inducible GAL1-10 promoter and includes c-terminal c-myc epitope and a six histidine epitope tag for purification.

FIG. 16 shows the results of running the soluble scFv's on polyacrylamide gels (top panel), all exhibiting an appropriate size for scFv's ranging from 28-35 kDs with expression levels ranging from 1-4 mg/ml. As shown in FIG. 17, when the RBE4 cells were labeled with these soluble scFvs, the A-group showed strong labeling of RBE4 cells and could also be internalized. On the other hand, the D-group scFvs and scFvF showed binding to RBE4 cells but were not internalized. The results of these experiments are summarized in the bottom panel of FIG. 16 and below.

Several of the class 1, 2, 3, 4, 5, 7, 10, 12, 15, 16, and 17 scFv were evaluated for their ability to mediate cellular internalization. The scFv were predimerized with the anti-cmyc epitope tag antibody to provide the bivalency often required for receptor clustering and endocytosis. The dimerized scFv were then applied to living RBE4 cells at 4° C. to yield cell surface labeling. Subsequently, the RBE4 cells were shifted to 37° C. for 30 minutes to enable cellular trafficking (FIGS. 17 and 20, data not shown for classes 4, 5, 7, 10, 12, 15, 16, and 17). Class 1, 4, 7, and 12 scFvs were rapidly internalized into vesicular structures within the RBE4 cells, whereas class 2, class 3, class 5, class 10, class 15, class 16, and class 17 scFvs bound the RBE4 surface but did not promote internalization. Control anti-fluorescein antibody (4-4-20) exhibited no binding or uptake. As suggested by the distinct internalization patterns, scFvA and OX26 do not compete for the same transport system. In addition, the transporter-scFvA interaction is not sensitive to glycosylation status as deglycosylation of RBE4 cells (mannosidase and neuraminidase) prior to binding and internalization had no observable effect. Further, the high homology of the scFvA clones B, C, G and K, shown in FIG. 12, indicates that members of this family may be equally effective in promoting internalization.

More specifically, RBE4 cells were labeled with pre-dimerized scFv A, scFv D, scFv 4-4-20 (dimerized to promote receptor clustering often required for endocytosis) or OX26 monoclonal antibody at 4° C. for cell surface labeling and then shifted to 37° C. to promote cellular trafficking. The cells were then labeled with AlexaFluor 555 conjugated anti-mouse IgG at 4° C. followed by AlexaFluor 488 conjugated anti-mouse IgG with or without cell permeabilization by saponin (SAP) treatment. Merged images of the AlexaFluor-labeled images are shown in FIG. 20. ScFvA exhibited both surface and intracellular labeling (compare scFvA labeling with (top left) and without (top middle) saponin treatment). In contrast, ScFvD (top right) exhibited only surface labeling upon saponin treatment. There was no labeling with 4-4-20 control scFv (bottom right). These results indicate that scFvA was rapidly internalized into vesicular structures within the RBE4 cells, whereas scFvD and scFvF bound the RBE4 surface but did not promote internalization. Similar results to that seen for scFvA were observed for classes 4 (scFvH), 7 (scFvE), and 12 (scFv4S21)). As a point of reference the OX26 MAb (FIG. 20, bottom left) has been demonstrated to endocytose and transcytose across brain endothelial cells in vitro and in vivo. As noted, FIG. 17 displays analogous data further illustrating micrographs of dual fluorescent staining of RBE4 binding scFv's showing specific binding and internalization of scFv A by RBE4 cells but not scFv D.

The inventors determined that class 1 scFv exhibited a clear binding signal with either supernatant or purified material at 3-4 μg/mL, but class 2 (scFvD) and 3 scFv (scFvF) required approximately 10-fold higher purified concentrations of 20-80 μg/mL to yield cell surface immunolabeling. In terms of binding affinity to live RBE4 cells, class 1 scFvA possessed an affinity of Kd=82±15 nM, whereas the affinity of class 2 scFvD as a monomeric protein could not be determined using this method. Instead, the inventors evaluated the binding properties of scFvD after predimerization with an epitope tag antibody (avidity=2.0±0.1 nM). As a comparison, the affinity of an anti-transferrin receptor scFv isolated using phagemid panning was measured to be 135 nM, of similar affinity to scFvA isolated with our yeast panning system.

FIG. 18 provides equilibrium binding attributes of scFvA and scFvD. The left panel of FIG. 18 depicts the binding isotherm for scFvA interaction with live RBE4 cells. The plot shows the fitted monomeric equilibrium binding functions and experimental data from two independent experiments. The right panel of FIG. 18 provides the binding isotherm for dimerized scFvD interaction with RBE4 cells. The plot shows the fitted monomeric equilibrium binding functions used to generate an apparent affinity (avidity) and experimental data from two independent experiments. Insets illustrate raw flow cytometry histograms that were used to generate the binding curves.

Thus, the results disclosed herein clearly indicate that yeast culture supernatants can be used directly for facile biochemical testing similar to approaches that use hybridoma-conditioned medium as a source for MAb. Further, the scFv can be purified for labeling and transport studies using the c-terminal six histidine epitope as described in EXAMPLE 11.

Example 10 Immunoprecipitation of Antigens for scFv

To assess the nature of the antigens recognized by the scFv, the inventors developed a novel yeast immunoprecipitation procedure. They used yeast displaying scFv to directly immunoprecipitate the cognate plasma membrane antigens from detergent-solubilized, biotinylated RBE4 lysates. Conveniently, the use of yeast as the immunoprecipitation particle allowed the sizing of antigens without any additional subcloning, production or immobilization of scFv proteins required by traditional immunoprecipitation methods. The inventors assessed the immunoprecipitated products by anti-biotin Western blotting (FIG. 19), and the low amount of background in such blots was a direct indicator of the specificity of the immunoprecipitation process. The antigens immunoprecipitated by class 1 scFvA (124 kDa-nonreduced, several large molecular weight bands-reduced), class 2 scFvD (104 kDa-nonreduced, 117 kDa-reduced) and class 6 scFvJ (122 kDa-nonreduced, 127 kDa-reduced) were distinct (FIG. 19). As predicted by the homology-based scFv class assignment, other class 1 scFv (scFvB, scFvC, scFvG and scFvK) yielded immunoprecipitation products identical to that seen for scFvA, and class 2 scFv I like that observed for class 2 scFvD (data not shown). The multiple bands appearing in the reduced scFvA sample suggest that along with the antigen recognized specifically by scFvA, co-immunoprecipitation of other biotinylated members of a protein complex or possibly multiple specific antigens may be occurring. Accordingly, scFv-antigen systems were identified that represent novel antibody-blood brain barrier transporter combinations that will form the basis for drug delivery.

Example 11 Purified scFvA Labels the Brain Vasculature In Vivo

The high-throughput method described so far allowed the identification of scFv clones that bind specifically to RBE4 cells and may be endocytosed in culture. However, the inventors wanted to confirm that clones identified in culture also bound brain endothelial cells in vivo. Therefore, it was necessary to first confirm that the antigen targeted by scFvA in culture was also present on the endothelial cells in vivo. FIG. 21 depicts the assessment of scFvA target antigen density and brain localization. Specifically, the left panel illustrates flow cytometric assessment of antigen density on RBE4 cells. Anti-transferrin receptor monoclonal antibody (OX26), IgG2a isotype control (not shown), pre-dimerized scFvA, pre-dimerized scFvD, and pre-dimerized control 4-4-20 scFv were used at antigen-saturating concentrations to label RBE4 cells in order to make direct comparisons of antigen density. The relative number of antigen sites present on the RBE4 cells was then assessed by flow cytometry. The scFvA antigen was present at approximately 3-fold higher levels than that found for scFvD, and 5.5-fold greater than that observed for the transferrin receptor. Also, the OX26 monoclonal antibody did not compete with scFvA in immunolabeling experiments, nor was the transporter-scFvA interaction sensitive to glycosylation status as deglycosylation of RBE4 cells (mannosidase and neuraminidase) prior to binding had no observable effect.

The right panel of FIG. 21 demonstrates that ScFvA preferentially recognizes the brain microvasculature. Co-localization of scFvA labeling with the highly brain capillary-specific lectin, Griffonia simplicifolia agglutinin (GSA) was complete and indicated that all brain blood vessels express the scFvA antigen. Frozen rat brain sections were co-labeled with scFvA (image 1) or 4-4-20 (image 4) and the brain endothelial cell marker GSA-FITC (images 2, 5). Images 3 and 6 are merged images indicating the overlap between scFv and GSA-FITC labeling. In contrast to scFvA, irrelevant scFv 4-4-20 did not yield any labeling. Similar results were observed for mouse brain sections and freshly isolated capillaries. Finally, much like the ranking of antigen density for RBE4 cultures, qualitative labeling intensities indicated that the scFvA antigen density in vivo was higher than that for the transferrin receptor (data not shown). The scale bar provided in image 3 is 50 μm in length. Therefore, scFvA specifically labels the vascular component of brain tissue in vivo and the antigen is of endothelial origin.

Example 12 Materials and Methods

The following provides a detailed description of the materials and methods utilized in the foregoing example sections.

Growth and Induction of scFv Library.

The nonimmune human scFv library in EBY100 yeast8 (a, GAL1-AGA1::URA3 ura3-52 trp1 leu2Δ1 his3Δ200 pep4::HIS2 prb1Δ1.6R can1 GAL) was grown at 30° C. in SD-CAA (20.0 g/L dextrose, 6.7 g/L yeast nitrogen base, 5.0 g/L casamino acids, 10.19 g/L Na₂HPO₄.7H2O, 8.56 g/L NaH₂PO₄.H₂O) plus 50 μg/mL kanamycin for 24 hours (OD600˜10). Yeast at 10-fold excess of the library diversity (5×10⁹) were subsequently induced in 500 mL SG-CAA medium (same as SD-CAA except dextrose replaced by galactose) at 20° C. for 22 hours prior to panning against RBE4 monolayers.

Panning of scFv Library Against RBE4 Cell Monolayers.

The RBE4 rat brain endothelial cell line was used as the brain endothelial cell source as RBE4 cells have previously been demonstrated to display many attributes characteristic of the BBB in vivo. RBE4 cells exhibit a nontransformed phenotype, express typical endothelial markers, respond to astrocyte cues, and exhibit BBB-specific properties such as the expression and correct localization of the tight junction protein occludin. In addition, plasma membrane-localized transporters characteristic to brain endothelial cells including those that transport glucose (GLUT1), large neutral amino acids (LAT1), and iron (transferrin receptor), and those that function in active efflux at the BBB (p-glycoprotein, MDR1), are expressed by RBE4 cells. RBE4 cells were a kind gift from Dr. Françoise Roux and were maintained as described previously. RBE4 cells were seeded on collagen type I-coated (Sigma) 6-well plates at 25% confluency two days prior to panning. Induced yeast cells at 10-fold excess of the library size (5×10⁹ yeast) were washed twice with 0.01 M PBS, pH 7.4, supplemented with 1 mM CaCl₂, 0.5 mM Mg₂SO₄ and 0.1% bovine serum albumin (BSA) (Wash buffer) and the yeast mixture was added dropwise onto 100 cm² of RBE4 cell monolayer to ensure even distribution across the monolayer. The density of yeast (5×10⁷ yeast/cm²) is at the upper limit for panning in that the yeast completely coat the RBE4 monolayer. Panning at high density allows ˜30% recovery of binding yeast while also providing appropriate oversampling of the library diversity. The monolayers were then incubated at 4° C. for 2 hours to allow yeast-RBE4 cell contacting. The washing strategy was optimized to recover a model scFv that binds to RBE4 cells with nanomolar affinity. The resulting method involved washing the RBE4 layers with ice cold wash buffer by gently rocking the plate twenty-five times, rotating the plate five times (repeated twice), and rotating the plate ten times. The washing supernatant was removed after each step and replaced with fresh wash buffer. After the washing steps, 1 mL of wash buffer was added into each well and all cells were scraped off the plate and pooled together. The yeast/RBE4 cell mixture was resuspended in 5 mL kanamycin-supplemented SD-CAA and grown at 30° C. overnight, followed by SG-CAA induction for 20 hours at 20° C. In parallel, a small fraction of the recovered cells were plated on SD-CAA agar plate to quantify the total number of recovered yeast cells after each round. Since the pool diversity was greatly reduced after round 1, the yeast panning density was lowered to 5×10⁶ yeast/cm², and the RBE4 area was reduced to 20 cm² for round 2 and 10 cm² for rounds 3-5. After round 2 of panning, the recovered yeast clones numbered 8.2×10⁴, and a parallel experiment with control yeast displaying an anti-fluorescein scFv (4-4-20) showed very little background using the same washing regimen indicating that the panning strategy was yielding primarily RBE4-binding yeast clones. To confirm that the yeast-RBE4 interactions were scFv-based, the scFv-encoding plasmids for several RBE4-binding yeast clones (7 from round 3, 12 from round 4) were recovered using the Zymoprep yeast miniprep kit (Zymo Research). The scFv-encoding plasmid was then retransformed into yeast surface display parent strain, EBY100, using the lithium acetate method and Trp+ transformants were selected. After RBE4 binding with the retransformed clones was confirmed, the plasmids were sequenced with the Gal1-10 (5′-CAACAAAAAATTGTTAATATACCT-3′; SEQ ID NO:35) and alpha terminator primers (5′-GTTACATCTACACTGTTGTTAT-3′; SEQ ID NO: 36) (UW-Madison Biotechnology Center).

High-Throughput Analysis of Recovered Yeast Clones.

As described above, yeast are typically grown first in SD-CAA followed by SG-CAA to promote scFv expression. However, this technique yielded comparatively low levels of scFv surface expression level and lowered percentages of yeast displaying scFv when a 96-well format was used. Therefore, the scFv display methodology was optimized for 96-well plates, and it was found that simultaneous growth and induction in SG-CAA allowed for scFv display having similar efficiency to that observed using the traditional yeast display methods. Thus, for high throughput screening, yeast clones were inoculated into 200 μL of SG-CAA (induced sample) and SD-CAA (control uninduced sample) in a 96-well plate and incubated at 30° C. for 24 hours. After removing 160 μl, of SD culture to ensure similar total yeast numbers as the parallel SG culture, the 96-well plate of yeast was centrifuged, and the supernatant was carefully removed. The yeast were then washed once with 150 μL wash buffer and resuspended in 150 μL wash buffer. In parallel, RBE4 cells cultured to confluency in a 96-well plate were washed once with ice-cold wash buffer. The yeast clones were then transferred into corresponding wells containing RBE4 monolayers and incubated at 4° C. for 2 hours. After washing, light microscopy was used to assess the binding capacity of the scFv yeast clones. After visual inspection, a yeast clone was defined as RBE4-binding if induced yeast remained bound while uninduced yeast originating from the same clone were washed away.

The scFv genes harbored by binding yeast clones were directly amplified by whole yeast cell PCR. Briefly, a small amount of a fresh, uninduced yeast colony was transferred into 30 μL 0.2% SDS, vortexed, frozen at −80° C. for 2 minutes and incubated at 95° C. for 2 minutes (temperature shift repeated once). One microliter of the cell lysis solution was then used as a PCR reaction template with primers, PNL6 Forward (5′-GTACGAGCTAAAAGTACAGTG-3′; SEQ ID NO: 37) and PNL6 Reverse (5′-TAGATACCCATACGACGTTC-3′; SEQ ID NO: 38). Subsequently, 20 μL of PCR product was subjected to BstNI (New England Biolabs) restriction digest at 60° C. for 14 hours. The digested products were resolved on a 3% agarose gel for unique scFv clone identification. The PCR product of each clone displaying a unique BstNI digestion pattern was sequenced with Rev Seq P2 (5′-CCGCCGAGCTATTACAAGTC-3′; SEQ ID NO: 39) and For Seq P2 (5′-TCTGCAGGCTAGTGGTGGTG-3′; SEQ ID NO: 40) primers. The sequence was then analyzed by the IgBLAST program to identify the human germline origin (IgBLAST available at NCBI website: www.ncbi.nlm.nih.gov).

Yeast Colony Northern Blotting.

Yeast colony Northern blotting was used to detect and presubtract class 1 and class 2 scFv from the yeast binding pool. Reagents and instruments were prepared as in standard Northern blotting experiments to eliminate RNase contamination. Yeast clones were cultured on SD-CAA agar plates and the resulting colonies were transferred onto ethanol-sterilized nitrocellulose membranes. The colony-loaded membrane was then layered on top of SG-CAA agar plates, cell side facing up, and incubated at 30° C. for 2 days to induce transcription of the scFv gene. To prepare the induced yeast colonies for Northern blotting, the nitrocellulose membranes were layered onto Whatman filter paper soaked with 10% SDS and incubated at 65° C. for 30 minutes. The filters were then fixed by transferring to formaldehyde-soaked filter paper at 65° C. for 30 minutes (3×SSC, 10% formaldehyde in ddH₂O). Air-dried membranes were subsequently baked for 2 hours at 80° C. under vacuum. Oligonucleotide probes corresponding to Class 1 VHCDR2 and Class 2 VHCDR2 were radiolabeled with a 10 residue 32^(P)-dATP tail using the STARFIRE kit according to manufacturer's instructions (IDT), and their specific radioactivity was determined by scintillation counting. Being part of the germline V-region, the VHCDR2 regions exhibited 100% homology within class 1 and class 2, and were therefore amenable to hybridization-based subtraction. The membranes were blocked in prehybridization buffer (50% formamide, 5×Denhardt's solution, 5×SSPE, 1% SDS, 0.1% salmon sperm DNA) at 43° C. for 2 hours, and then hybridized (prehybridization buffer with 8×105 cpm/ml of each probe) at 43° C. overnight. After hybridization, the nitrocellulose membranes were washed as follows: 2×SSC, 0.1% SDS at room temperature for 8 minutes, 0.5×SSC, 0.1% SDS at room temperature for 8 minutes, 0.1×SSC, 0.1% SDS at room temperature for 8 minutes, 0.1×SSC, 1% SDS at 50° C. for 30 minutes. The membranes were then exposed to ECL Hyperfilm (Amersham) at −80° C. for 24 or 72 hours. Although VHCDR2 was used as the probe in these subtractive screens, the diversity of the recovered scFv clones can be readily expanded as desired via subtraction using any combination of CDR probes.

scFv Secretion and Purification.

Open reading frames for scFv were isolated from the PCR products used for BstNI typing by NheI-HindIII restriction digest and were shuttled to an scFv yeast secretion vector (pRS316-GAL4-4-20) that has been used extensively for scFv secretion. The resultant pRS316-GALscFv plasmids were then transformed into YVH10, a yeast strain overexpressing protein disulfide isomerase. Yeast harboring scFv secretion vector were grown in minimal SD medium (2% dextrose, 0.67% yeast nitrogen base) supplemented with 2×SCAA amino acid (190 mg/L Arg, 108 mg/L Met, 52 mg/L Tyr, 290 mg/L Ile, 440 mg/L Lys, 200 mg/L Phe, 1260 mg/L Glu, 400 mg/L Asp, 480 mg/L Val, 220 mg/L Thr, 130 mg/L Gly, 20 mg/L tryptophan lacking leucine and uracil) at 30° C. for 72 hours. Subsequently, scFv secretion was induced at 20° C. for 72 hours in SG-SCAA (dextrose substituted by galactose) with 1 mg/ml BSA as a nonspecific carrier. For experiments requiring purified scFv, Ni-NTA columns (Qiagen) were used to purify the six histidine-tagged scFv from 50 mL or 1 L batches as described previously in the literature.

The size, purity, and secretion yields of scFv were analyzed by SDS-polyacrylamide gel electrophoresis (PAGE) with a 4% stacking and 12.5% separating gel followed by Coomassie blue staining. Protein concentrations were estimated by comparison to a series of carbonic anhydrase standards (31 kDa) and by BCA protein assay (Pierce). In parallel, the SDS-PAGE resolved proteins were also blotted onto a nitrocellulose membrane (BioRad) for Western blotting. The nitrocellulose membrane was blocked at 4° C. overnight in TBST solution (8 g/L NaCl, and 0.1% Tween-20, buffered to pH 7.6 with 20 mM Tris) supplemented with 5% nonfat milk and probed with 1 μg/mL 9E10 anti c-myc antibody (Covance) followed by an anti-mouse IgG horse radish peroxidase conjugate (Sigma). Detection was performed using enhanced chemiluminescence and multiple time point exposures to ECL hyperfilm (Amersham) were evaluated by NIH ImageJ software for quantification.

Affinity Determination.

RBE4 cells were labeled at various scFvA concentrations at 4° C., and the bound scFv detected by anti-cmyc (9E10) antibody labeling followed by anti-mouse IgG AlexaFluor 555. Fluorescence intensity was monitored by FACSCalibur flow cytometer and used to quantitate fractional bound ligand. The scFvA binding data was fit to an equilibrium binding model to determine the monovalent affinity dissociation constant (Kd). The cell-labeling assay was not sensitive enough to produce a binding curve using monomeric scFvD, so scFvD was predimerized with anti-epitope tag antibody, 9E10, to provide the requisite avidity for the ligand binding measurements. ScFv D dimer-labeled cells were then probed with anti-mouse IgG AlexaFluor 555 conjugate and assessed by flow cytometry. The resulting data were fit to an equilibrium binding model to derive an apparent affinity (avidity). For antigen density experiments, living RBE4 cells were labeled at 4° C. with 62.5 nM of pre-dimerized scFvA, scFvD, 4-4-20 scFv, OX26 monoclonal antibody, or IgG2a isotype control. A uniform secondary antibody (anti-mouse IgG AlexaFluor 555 conjugate) was used for each sample to facilitate quantitative comparisons of labeling intensity. These antibody labeling concentrations were adequate for saturation binding of the cell surface antigens, and the cell surface labeling was quantitatively assessed by flow cytometry.

ScFv-RBE4 Immunocytochemistry.

Predimerization of scFv via the c-myc epitope tag by the 9E10 antibody was used as a method to provide bivalency which is often an important component for promoting cellular internalization of scFv. To this end, the RBE4-binding scFv was first incubated with 9E10 to form artificial dimers. Equal volumes of purified scFv (diluted to 8 μg/mL for scFvA or 32 μg/mL for scFvD and 4-4-20 using 40% goat serum in PBS supplemented with 1 mM CaCl₂, 0.5 mM Mg₂SO₄) and 10 μg/mL 9E10 were mixed and incubated at room temperature for 1 hour to form artificial dimer RBE4 cells at about 90% confluency were washed 3× with wash buffer. RBE4 cells were then incubated with scFv artificial dimer or OX26 monoclonal antibody (10 μg/mL) (Serotec) at 4° C. for 30 minutes and then switched to 37° for another 30 minutes. An anti-mouse IgG secondary antibody conjugated with AlexaFlour555 (Molecular Probes) was applied for 30 minutes at 4° C. to label cell surface-bound scFv. The cells were then permeabilized with 0.5% saponin (SigmaAldrich) diluted in wash buffer at 4° C. for 5 minutes, and subsequently labeled with an anti-mouse IgG antibody conjugated with AlexaFluor488 (Molecular Probes) for 30 minutes at 4° C. to detect internalized scFv. Labeled cells were then fixed with 4% paraformaldehyde and examined using a fluorescence microscope (Olympus IX70).

Yeast Display Immunoprecipitation.

ScFv-displaying yeast cells selected from the human scFv library were directly used to immunoprecipitate the cognate plasma membrane antigens. Yeast cells displaying anti-hen egg lysozyme (D1.3) scFv were used as a negative control. As a positive control, an anti-transferrin receptor OX26 scFv yeast display plasmid was created by excising OX26 scFv open reading frame from pRS316-GALOX26 as an NheI-XhoI fragment and ligating into pCT-LWHI. Yeast clones were grown and induced in 50 mL cultures as described above. Induced yeast were collected by centrifugation, washed and fixed with 3% vol/vol formalin in PBS. RBE4 plasma membrane proteins were biotinylated using 0.5 mg/mL Sulfo-NHS-LC-Biotin (Pierce). To prepare RBE4 cell lysate, approximately 5×10⁶ biotinylated RBE4 cells were lysed using a 1% (w/v) n-octyl-beta-D-glucopyranoside (scFvA, B, C and J Sigma) or 0.1% (w/v) Triton X-100 (scFvD, I, J, and OX26, Sigma) detergent solution in PBS, supplemented with a protease inhibitor cocktail (Calbiochem). For immunoprecipitation, 400 μg of cell lysate protein was mixed with approximately 10⁸ yeast cells and incubated overnight at 4° C. Elution of immunoprecipitated product was performed by resuspending yeast cells in 30 μL of 0.5% SDS in 0.4 M Tris (pH 6.8) for 15 minutes. The eluates were separated with SDS-PAGE (8% separating gel) with or without reducing agent (DTT) present, and blotted onto a nitrocellulose membrane (BioRad). Western blotting was subsequently performed with an anti-biotin monoclonal antibody (0.5 μg/mL, clone BTN.4, Labvision), OX26 monoclonal antibody (5 μg/mL, Serotec), or anti-insulin receptor

-subunit monoclonal antibody (1 μg/mL, clone CT-3, Labvision) as described above. Neither scFvA nor scFvD were active in Western blotting format with immunoprecipitated products or with cell lysates, likely a result of selections being performed under native conditions with living cells.

Immunohistochemical Labeling of Rat Brain Sections by scFv A.

Brain tissue sections were prepared from the brain of an adult male Sprague Dawley rat. The brain was snap-frozen with tissue freezing medium (Triangle Biomedical Sciences) using a liquid nitrogen bath, and 7 μm coronal sections were cut from the frozen brain. The brain sections were blocked with 40% goat serum and 0.2% TritonX-100 in PBSCM at room temperature for 30 minutes. Purified scFv A or 4-4-20 was diluted with 40% goat serum and incubated with an equal volume of 10 μg/mL 9E10 for 1 hour at room temperature to form artificial dimer. Brain sections were then incubated with scFv A artificial dimer at 4° C. for 1 hour. A secondary labeling solution consisting of phycoerythrin-conjugated anti-mouse IgG and FITC conjugated Griffonia simplicifolia lectin (GSA-FITC 10 μg/ml, Sigma) was applied for 30 minutes at 4° C. After washing, the brain sections were immediately fixed with 4% paraformaldehyde for 10 minutes on ice and examined by fluorescence microscopy.

Example 13 Improved Immunoprecipitation Method for Isolating and Characterizing Antigens

In the above Examples, yeast library screening methods were used to identify antibodies against cell surface antigens. Specifically, the inventors have demonstrated that yeast cells displaying scFvs can be used for immunoprecipitation and characterization by Western blotting of target cell (RBE04) surface antigens (see Examples 10 and 12). In this Example, the inventors show the full capability of the yeast display immunoprecipitation technique (YDIP) for recovery and analysis of both soluble and plasma membrane antigens. Specifically, the inventors report the use of YDIP with tandem mass spectrometry to identify the RBE4 plasma membrane antigen immunoprecipitated by scFvJ as the neural cell adhesion molecule (NCAM).

Materials and Methods:

Cells, media and plasmids. Saccharomyces cerevisiae strain EBY100 was used for surface display of scFvs. Surface display plasmids pCT201-D1.3 and pCT302 were used for the display of anti-hen egg lysozyme D1.3 scFv and anti-fluorescein 4420 scFv, respectively. All human scFvs (scFvA, scFvD, scFvJ, and scFvK) in the surface display format were selected from the previous examples. Yeast cells were grown in SD-CAA medium (20.0 g/L dextrose, 6.7 g/L yeast nitrogen base, 5.0 g/L casamino acids, 10.19 g/L Na2HPO4.7H2O, 8.56 g/L NaH2PO4.H2O) at 30° C. to reach an OD600 nm of approximately 1.0 and induced in the same volume of SG-CAA medium (dextrose replaced by galactose in SD-CAA) for 16-18 h at 20° C. for scFv display. The rat brain endothelial cell line (RBE4) was a kind gift from Dr. Françoise Roux. RBE4 cells were grown at 37° C. in 5% CO2, in 45% Alpha Minimum Essential Medium, 45% Ham's F10 medium, and 10% heat inactivated fetal bovine serum (FBS, Invitrogen, Carlsbad, Calif.) supplemented with 100 μg/mL streptomycin, 100 units/mL penicillin G (Invitrogen, Carlsbad, Calif.), 0.3 mg/mL geneticin (Fisher Scientific, Pittsburgh, Pa.) and 1 μg/L basic FibroblastGrowth Factor (bFGF) (Roche Diagnostics, Indianapolis, Ind.).

Preparation of biotinylated RBE4 cell lysates. Plasma membrane proteins of RBE4 cells were biotinylated by incubating live RBE4 cells with 0.5 mg/mL sulfo-NHS-LCBiotin (Pierce, Rockford, Ill.) in 10 mM phosphate buffered saline (PBS, pH 7.4) supplemented with 1 mMCaCl2, 0.5 mM Mg2SO4 (PBSCM) for 30 min with rocking at room temperature. The charged sulfoxide group of the biotinylating reagent prevents the biotinylation of cytosolic proteins by hindering the diffusion through cell membranes. After the biotinylation, approximately 5×106 biotinylated RBE4 cells were lysed at 4° C. by scraping the cells into 1 mL of PBS supplemented with a protease inhibitor cocktail (Calbiochem, Gibbstown, N.J.), 2 mM EDTA and containing one of the following detergents: 0.1% (w/v) Triton X-100 (TX), 1% (w/v) n-octyl-β-D-glucopyranoside (OG) (Anatrace, Maumee, Ohio), 0.5% w/v) CHAPS (Fisher Scientific), or radioimmunoprecipitation assay (RIPA) buffer (0.1% (w/v) SDS, 0.5% (w/v) sodiumdeoxycholate (DOC), and 1% (w/v) Triton X-100 in PBS). The initial cell lysates were then centrifuged at 18,000×g for 15 min at 4° C. to remove insoluble debris. The total protein concentration remaining in the supernatant was determined using the BCA assay per manufacturer's instructions (Pierce, Rockford, Ill.).

Detection of scFv activity in detergent solutions. To assess the effects of detergents on scFv affinity, an anti-hen egg lysozyme antibody D1.3 scFv and hen-egg lysozyme (HEL) from chicken egg white (Sigma, St. Louis, Mo.) were used. Yeast cells were fixed with 3% v/v formaldehyde in PBS for 1 h at room temperature when indicated. The HEL was biotinylated using sulfo-NHS-LC-biotin (Pierce, Rockford, Ill.) and the degree of biotinylation was determined to be 2.1 biotins per HEL using the 4-Hydroxyazobenzene-2-carboxylic acid (HABA) assay (Sigma, St. Louis, Mo.). Serial dilutions of HEL were prepared in the various lysate buffers described above minus protease inhibitors and incubated with yeast cells displaying anti-HEL D1.3 scFv for 2 h at 20° C. The incubated yeast cells were washed once with the corresponding detergent solution, once with PBS containing 0.1% (w/v) bovine serum albumin (PBS-BSA) and subsequently incubated with a mouse anti-c-myc antibody (9E10, 30 μg/mL, Covance, Berkeley, Calif.) to selectively analyze the antibody-displaying yeast population. Next, goat antimouse IgG-Alexa488 conjugate (αM488, 1/1000 dilution, Invitrogen, Carlsbad, Calif.) and streptavidin-phycoerythrin conjugate (SAPE, 1/80 dilution, Sigma) were added to quantify ligand binding. All of the washing and labeling steps were performed at 4° C. The fluorescence intensities were quantified using the FACSCalibur flow cytometer (Becton Dickinson, Franklin Lakes, N.J.) and fitted to a bimolecular equilibrium binding model to determine the dissociation constants (Kd). To test the binding activity of scFvA, scFvK, scFvD, and scFvJ, yeast displaying scFv were incubated with biotinylated RBE4 cell lysate (1% OG, 200 μg total protein) for 2 h at 4° C. Yeast were then washed twice with PBS containing 1% OG. Labeling with 9E10, SAPE, and αM488 was identical to that described above, except for scFvJ, for which mouse anti-HA antibody (12CA5, Roche Diagnostics, Indianapolis, Ind.) was used instead of 9E10, since scFvJ is actually a single domain Fv consisting of only the variable heavy chain and lacking the C-terminal c-myc epitope. To measure the relative affinity of scFvA and scFvK, all procedures were identical as in measuring affinity of D1.3 scFv, except that serially diluted RBE4 cell lysate (biotinylated, 1% OG) was used as a ligand source.

Yeast Display Immunoprecipitation.

Immunoprecipitation from complex mixtures. Approximately 5×10⁷ of yeast cells displaying D1.3 scFvs were used for YDIP. Yeast cells were fixed with 3% v/v formaldehyde in PBS for 1 h at room temperature when indicated. Yeast were incubated 2 h at 4° C. with 34 nM HEL diluted into RBE4 cell lysate prepared with 1% (w/v) TX and washed twice with and eluted with 50 μL of 0.2 M glycine-HCl solution (pH 2.0). Yeast displaying the anti-fluorescein 4-4-20 scFv were used as a negative control.

Elution methods for antigen recovery. To monitor the amount of antigen obtained by various elution methods, D1.3 scFv and biotinylated HEL were used. A batch of 3×10⁷ yeast cells displaying D1.3 scFv were incubated with 10 nM HEL in PBS-BSA for 2 h at 4° C. The yeast cells were washed twice with PBS at 4° C. prior to elution. Elution of immunoprecipitated product was performed by resuspending yeast cells in 30 μL of 0.2M glycine-HCl solution (pH 2.0), 9 M urea, 0.2 M NaOH, 3 M NaCl, or 0.2% (w/v) SDS for 10 min at 4° C. Where indicated, yeast cells were fixed with 3% v/v formaldehyde in PBS for 1 h at room temperature before incubation with the antigen, to reduce the co-elution of yeast proteins. The eluates were separated with SDS-PAGE (15% separating gel) and either probed with streptavidin-HRP conjugate (1/2000 dilution, GE healthcare, Piscataway, N.J.) or silver-stained following standard protocols. The HEL bands from Western blot films or silver stained gels were quantified using densitometry with ImageJ (US National Institutes of Health, Bethesda, Md.) to compare the relative amount of biotinylated HEL eluted under each condition.

Immunoprecipitaion of cell surface antigens and Western Blotting. For Western blotting analysis of immunoprecipitated antigens, 3-10×10⁷ yeast cells were used. Induced yeast cells were collected by centrifugation and washed with PBS-BSA. Biotinylated RBE4 cell lysate prepared using the various detergents containing approximately 400 μg of total protein (corresponding to approximately 2×106 RBE4 cells) was mixed with yeast cells and incubated overnight at 4° C. in a total volume of 200 μL. After the incubation, yeast cells were washed three times by resuspension in 1 mL of the corresponding lysis buffer (without protease inhibitor cocktail) and incubated for 15 min at 4° C. Elution of immunoprecipitated product was performed by resuspending yeast cells in 30 μL of 0.2 M glycine-HCl solution (pH 2.0) for 10 min. The mixtures were briefly centrifuged and the eluted supernatants were separated with non-reducing SDSPAGE (8% separating gel), and blotted onto a nitrocellulose membrane (BioRad, Hercules, Calif.). Yeast displaying D1.3 scFv were used as a negative control for these experiments. Western blotting was subsequently performed with an anti-biotinmonoclonal antibody (0.5 μg/mL, clone BTN.4, Labvision, Fremont, Calif.). To test the serial elution process, scFvJ was used. The IP procedure is identical to that above except the eluted supernatant was serially applied for the indicated number of times to elute additional batches of yeast that have undergone the immunoprecipitation process. To confirm the scFvJ antigen neural cell adhesion molecule (NCAM), a monoclonal anti-NCAM antibody (clone 5B8, Developmental studies Hybridoma Bank, Iowa Cities, Iowa) was used for Western blotting.

Identification of immunoprecipitated proteins using tandem mass spectrometry. To sequence hen-egg lysozyme using tandem mass spectrometry (MS/MS), approximately 3×108 yeast displaying the D1.3 scFv were incubated for 2 h at 4° C. with 30 nM HEL in PBSTX, washed twice with PBSTX and eluted with 50 μL of 0.2 M glycine-HCl solution (pH 2.0). The elution product was precipitated for 2 h by adding 250 μL of ice-cold acetone at −20° C. The protein pellet was dried and reconstituted in 5 μL of 8 M urea and then diluted with 40 μL of 50 mM ammonium bicarbonate buffer with 10 mM DTT. Approximately 100 ng of sequencing grade modified trypsin (Promega, Madison, Wis.) was added and digestion was allowed to proceed for 16 h at 37° C. Peptide fractions were individually analyzed by nanoLC-MS/MS using 1100 series LC/MSD Trap SL spectrometer (Agilent, Palo Alto, Calif.). Chromatography of peptides prior to mass spectral analysis was accomplished using C18 reverse phase HPLC trap column (Zorbax 300SB-C18, 5 μM, 5×0.3 mm, Agilent) and separation column (Zorbax 300SB-C18, 3.5 μm, 0.075×150 mm, Agilent) onto which 40 μL of each extracted peptide fraction was automatically loaded. An Agilent 1100 series HPLC delivered solvents A: 0.1% (v/v) formic acid in water, and B: 95% (v/v) acetonitrile, 0.1% (v/v) formic acid at either 10 μL/min, to load sample, or 0.28 μL/min, to elute peptides directly into the nano-electrospray source over a 60 min 20% (v/v) B to 80% (v/v) B gradient. As peptides eluted from the HPLC-column/electrospray source, MS/MS spectra were collected over 5 channels from 300 to 2200 m/z; redundancy was limited by dynamic exclusion (120 s). MS/MS data were converted to mgf file format using Data Analysis Software (Agilent). Resulting mgf files were used to search the nonredundant NCBI database with an in-house licensed Mascot search engine (Matrix Science, London, UK) with methionine oxidation, cysteine carbamidomethylation and glutamine and asparagine deamidation as variable modifications.

For MS/MS sequencing of the RBE4 cell-surface antigen recognized by scFvJ, 3×109 formaldehyde fixed yeast cells displaying scFvJ were divided into eight microfuge tubes and RBE4 cell lysate containing 3 mg of total protein (both biotinylated and non-biotinylated ID was successful) in 1 mL of 1% OG with protease inhibitors was added to each tube. The yeast cells were incubated overnight at 4° C. in the cell lysate, and then 4 product pools created each by serial elution of two tubes with 70 μL of 0.2 M glycine-HCl solution (pH 2.0). To concentrate the antigen, the four elution products were combined and precipitated at 4° C. for 2 h by the addition of trichloroacetic acid (Fisher Scientific) to a final concentration of 13% (w/v). Protein was pelleted by centrifuging at 12,000×g for 15 min at 4° C. The pelleted protein was then dissolved in 2× Laemmli sample buffer for separation by SDS-PAGE (8%). Gels were stained using colloidal coomassie to visualize the eluted proteins. In-gel digestion was performed using standard protocols. In short, gel pieces were excised, dehydrated, and reduced in 50 μL 25 mMDTT in 25 mM ammonium bicarbonate for 20 min at 56° C., and alkylated with 50 μL of 55 mM iodoacetamide (Sigma, St. Louis, Mo.) in 100 mM ammoniumbicarbonate for 20 min at room temperature. Then the gel pieces were washed, dried and digested for 18 h at 37° C. with 400 ng of sequencing grade modified trypsin in 25 mM ammonium bicarbonate with 5% (v/v) acetonitrile. Digested peptides were eluted off from a C18 micro ZipTip (Millipore, Billerica, Mass.) with acetonitrile/H2O/TFA (60%:40%:0.2%) directly onto the Opti-TOF™ 384 Well plate (Applied Biosystems, Foster City, Calif.) and re-crystallized with 0.75 μL of matrix Y. K. Cho et al./Journal of Immunological Methods 341 (2009) 117-126 119 (10 mg/ml α-Cyano-4-hydroxycinnamic acid in acetonitrile/H2O/TFA (70%:30%:0.2%)). Peptide identification via result dependent MS/MS analysis was performed on a 4800 Matrix-Assisted Laser Desorption/Ionization-Time of Flight-Time of Flight (MALDI TOF-TOF) mass spectrometer (Applied Biosystems, Foster City, Calif.). In short, a peptide fingerprint was generated by scanning the 700-4,000 Da mass range using 1500 shots acquired from 20 randomized regions of the sample spot using an OptiBeam™on-axis Nd:YAG laser (4200 intensity, 200 Hz firing rate, 3-7 ns pulses). The fifteen most abundant precursors, excluding trypsin autolysis peptides and sodium/potassium adducts, were selected for subsequent tandem MS analysis where 2000 total shots were taken with 4700 laser intensity and 2 kV collision induced activation (CID) using air. Post-source decay (PSD) fragments from the precursors of interest were isolated by timed-ion selection and reaccelerated into the reflectron to generate the MS/MS spectrum. Raw data was deconvoluted using GPS Explorer™ software and submitted for peptide mapping and MS/MS ion search analysis against non-redundant NCBI database with an in-house licensed Mascot search engine (Matrix Science, London, UK) with fixed modification of carboxyamidomethylation of cysteines and parent/fragment ion mass tolerance of 0.3 Da.

Quantitation of scFv and NCAM expression levels using flow cytometry. To quantitate the expression level of scFvs on the yeast cell surface, Quantum simply cellular anti-mouse IgG microbeads (Banglabs, Fishers, Ind.), which contain four populations of beads with known mouse IgG binding sites were used. Yeast cells displaying either D1.3 scFv or scFvA were incubated with a mouse anti-c-myc antibody (9E10, 30 μg/mL, Covance, Berkeley, Calif.) in PBS-BSA for 1 h. For scFvJ quantitation, a mouse anti-HA antibody (12CA5, Roche Diagnostics, Indianapolis, Ind., 1/100 dilution) was used instead. The microbeads were also incubated under the same conditions. Next, the yeast cells and the microbeads were washed, incubated with a goat anti-mouse IgG-Alexa555 conjugate (1/500 dilution, Invitrogen, Carlsbad, Calif.) for 30 min. and analyzed using the FACSCalibur flow cytometer. To quantitate the expression level of NCAM in RBE4 cells, RBE4 cells were permeabilized with 0.5% (w/v) saponin in PBSCM with 40% (v/v) goat serum (PBSCMG, Sigma, St. Louis, Mo.) and incubated with a mouse anti-NCAM antibody (clone 5B8, diluted to 50 μg/mL) in PBSCMG for 1 h. The microbeads were also incubated under the same conditions. The secondary reagents used were identical to the scFv quantitation.

Results:

Effect of Detergents on yeast-displayed scFv binding activity. Yeast display immunoprecipitation (YDIP) takes advantage of scFv expressed as fusions to the yeast cell wall for capture of antigens from complex mixtures such as cell lysates (FIG. 22). Since creation of solubilized protein mixtures in the form of lysates requires the use of detergents (FIG. 22 step 1), particularly for the solubilization of membrane proteins, the scFv used in YDIP must retain their binding activities in the presence of detergents. Thus, as a model system, the affinity of yeast surface-displayed anti-hen egg white lysozyme (HEL) scFv (D1.3) for its HEL ligand was assessed in various detergent solutions. Detergents tested included 1% (w/v) Triton X-100 (TX), 1% (w/v) n-octyl-β-Dglucopyranoside (OG), 0.5% (w/v) CHAPS, and 0.1% (w/v) SDS as well as a mixture of detergents (0.1% (w/v) SDS, 0.5% (w/v) sodium deoxycholate (DOC), and 1% (w/v) Triton X-100), which composes the radio-immunoprecipitation assay (RIPA) buffer. The concentrations of detergents were chosen to be higher than the critical micelle concentration (CMC) of each detergent, since complete solubilization of cell membranes generally occurs above the CMC. The D1.3 scFv remained active with comparable affinity for HEL to that found in PBS-BSA control buffer, varying byat most 3-fold (FIG. 23A, Table 1).

TABLE 1 Affinity of D1.3-HEL interaction in detergent solutions PBS additives K_(d) (nM) BSA 1.07 ± 0.03 TX 0.488 ± 0.03  OG 2.61 ± 0.54 CHAPS 1.80 ± 0.16 RIPA 3.43 ± 0.15 Reported Kd = 1.37 ± 0.14 nM (VanAntwerp and Wittrup, (2000) The lone exception was SDS, which resulted in a complete inhibition of the antigen-antibody interaction. Interestingly however, when 0.1% SDS was mixed with 1% TX and 0.5% DOC as in the RIPA buffer, the scFv remained active (FIG. 23A). In addition to maintaining the nanomolar binding affinity, it was important to determine the amount of antigen that can be immunoprecipitated under each detergent condition, or in other words the percentage of scFvs that remain active. The levels of antigen-antibody interaction were compared at saturating concentrations of HEL (142 nM) in each detergent solution. Compared to the displayed scFvs binding to HEL in PBS-BSA, with the aforementioned exception of SDS, more than 75% of the scFvs remained active in terms of the amount of antigen that can be immunoprecipitated (FIG. 23B).

ScFvs (scFvA, scFvK, scFvD, and scFvJ) that were previously selected as capable of binding to rat brain endothelial cell line (RBE4) plasma membrane proteins (see previous Examples) were used to assess the general compatibility of yeast displayed scFv for immunoprecipitation both from the standpoint of detergent tolerance and applicability to membrane protein targets. Yeast cells displaying these scFvs were used to immunoprecipitate antigens from RBE4 cell lysates generated by TX detergent-solubilization of biotinylated plasma membranes (FIG. 22, steps 1-3). Using flow cytometry, significant antigen-antibody interaction was detected for yeast cells displaying scFvA, scFvK, scFvD, and scFvJ (FIG. 22, step 4) while no interaction was detected for yeast cells displaying an irrelevant scFv (FIG. 23C). Similar results were obtained by using cell lysates generated by OG-mediated solubilization (data not shown and FIG. 23C inset). Moreover, Western blotting using an anti-biotin antibody indicates the presence of specific immunoprecipitation products, and since biotinylated rat proteins are not evident in the immunoprecipitation product using yeast displaying irrelevant antibody, the preparations are quite clean (FIG. 23C inset). In addition, since antigen-antibody interactions can be accurately quantified on the yeast surface, important antibody characteristics such as relative affinity could be rapidly determined using YDIP (FIG. 22, step 4). As an example, scFvA and scFvK yield the same immunoprecipitation product (FIG. 23C inset) and these antibodies differ by only six amino acids in the light-chain of CDR3 (FIG. 23D). To rapidly compare these two antibody clones, an affinity titration on the surface of yeast using biotinylated cell lysates was performed and it was determined that scFvA has a two-fold improved affinity compared with scFvK under these conditions (FIG. 23D). Notably, the relative affinity was determined by direct titration of the cell lysate, thereby eliminating the process of antigen purification, which is often a challenge for cell-surface antigens. These results suggest that yeast displayed displaying scFvs retain their binding activities in various detergent solutions and that YDIP is effective in antigen isolation and characterization of antigen-antibody interactions.

Elution, antigen purity and quantity by YDIP. Next, we further assessed the purity and quantity of antigens isolated using YDIP under a variety of elution conditions. The anti-HEL D1.3 scFv was again tested as a model system representing an antibody-soluble antigen combination. We first sought to identify the most efficient method for dissociation of bound antigens using YDIP of biotinylated HEL from a buffer solution (FIG. 22 step 5). Since it is known that various yeast cell wall proteins are also extracted from yeast under the elution conditions tested here, we assessed each elution condition not only in terms of recovered antigen quantity but also antigen purity relative to coextracted yeast proteins. Tested elution conditions included low pH (0.2 M glycine-HCl, pH 2.0), high pH (0.2 M NaOH), 9 M urea, high salt (3M NaCl), and 0.2% (w/v) SDS. Each method resulted in elution of antigen; however, it was immediately apparent that the amount of coextracted yeast protein was substantial (data not shown). Thus, to reduce the amount of coextracted yeast protein, yeast cells were first fixed/crosslinked with a 3% formaldehyde solution prior to YDIP (FIG. 22, step 2). Using fixed yeast cells for YDIP, there was no significant effect on D1.3 scFv binding affinity and a small 10-20% decrease in HEL capture (FIGS. 23A and B). For elution of immunoprecipitated HEL from fixed yeast, the low pH, SDS and urea elution methods had comparable efficiencies, while high pH and high salt were less effective (FIG. 24A). In addition, the amount of coextracted yeast protein was significantly diminished by yeast fixation, with low pH elution having the least amount of coextracted protein (data not shown). Since low pH elution gave excellent yields and minimal yeast protein background, it was generally used as the elution method.

In addition to coextracted yeast proteins, another confounding factor for antigen analysis is the non-specific binding of mammalian cell lysate proteins to yeast. Lysate-derived impurities can be more detrimental than the coextracted yeast proteins in applications such as antigen identification, since yeast proteins can be distinguished from mammalian proteins by sequence in many cases, while contaminants from the same species cannot. To evaluate lysate-derived impurities, YDIP was performed to recover HEL that had been doped into RBE4 cell lysates. First, using unfixed yeast, several bands other than HEL were detected on a silver-stained gel, especially in the lower molecular weight range (FIG. 24B lanes 1 and 2), yielding an HEL purity of approximately 50-60%. For the most part, these proteins did not appear to be lysate-derived as many of the same contaminants were detected in the YDIP of HEL in the experiments described above where lysate was absent (data not shown). Upon yeast fixation, the purity increased to 80% with both yeast and lysate contaminants taken into account (FIG. 24B lane 4). Combined with the anti-biotin Western blotting results for scFvA, scFvK, scFvD, and scFvJ (FIG. 23C inset), these results show that proteins in RBE4 cell lysate have minimal non-specific binding to yeast. Finally, the immunoprecipitation of HEL from solution was specific to the yeast displaying D1.3 scFv and was not detected with yeast displaying an irrelevant scFv (FIG. 24B).

Another important aspect to consider is the amount of antigen isolated, because 50-500 ng are desired for characterization by peptide sequencing using MS/MS. We first estimated the quantity of antigen that could be reasonably isolated using YDIP. Using the HEL-D1.3 pair that has an affinity of Kd=0.488 nM in TX lysate (Table 1) with 31,000 scFv per yeast cell (see Materials and methods for scFv quantification details) and 10 nM or higher antigen concentration, approximately 150 ng of antigen can be isolated with 3×108 D1.3-displaying yeast cells (15 mL overnight culture with density of 2 OD600 nm). Using 5×107 yeast cells (˜3 mL overnight culture), as was the case in FIG. 3B, it was thus predicted that 25 ng of HEL could be immunoprecipitated from an RBE4 cell lysate containing a 34 nM concentration of HEL. In practice, approximately 18 ng of HEL was immunoprecipitated (FIG. 24B lane 2) representing 70% of the theoretical yield. Therefore, using 10-100 mL of overnight yeast display cultures for YDIP is sufficient to isolate antigens in amounts suitable for downstream characterization.

YDIP of mammalian cell-surface antigens. Since YDIP exhibited good recovery and purity for the soluble HEL antigen, the optimized YDIP protocol was applied to analyze plasma membrane antigens. We have shown that yeast cells displaying scFvs selected from a non-immune human scFv library can be used to immunoprecipitate mammalian cell surface antigens from cell lysates for Western blot analysis using various detergents and elution conditions (FIG. 23). However, unlike the case of a soluble antigen like HEL, the plasma membrane antigen was being isolated from cell lysates in low nanogram quantities that could not be detected by either silver/coomassie staining or MS/MS. The reduced recovery of antigen was likely a combined result of both antigen expression levels and reduced antibody affinities (80-1000 nM) compared with the high affinity D1.3 scFv. Therefore, to increase the YDIP yield as well as antigen concentration for downstream applications, we adapted a ‘serial elution’ method in which a single small volume of elution buffer is used to serially elute multiple batches of yeast cells each used to immunoprecipitate antigen from fresh cell lysate. Using scFvJ displaying yeast with OG-solubilized RBE4 cell lysate, YDIP was performed. Here, OG was used for the lysis due to its compatibility with MS/MS analysis. ScFvJ immunoprecipitates an antigen of approximately 130 kDa (FIG. 23C), and serial elution effectively increased the antigen amount and concentration nearly 20-fold over a single elution approach (FIGS. 25A and B). After 4 elutions, little increase in eluted antigen is seen since the pH buffering capacity of 0.2M glycine-HCl becomes limiting. While antigen concentration increases dramatically, selectivity of the YDIP process is maintained as the level of irrelevant biotinylated lysate proteins isolated during the procedure remains very low (FIG. 25).

Identification of immunoprecipitated proteins using tandem mass spectrometry. To assess the compatibility of YDIP with mass spectrometry for peptide sequencing and antigen identification, we first tested the D1.3-HEL system. To this end, HEL was immunoprecipitated from a TX containing buffer using 3×10⁸ formaldehyde-fixed yeast cells. HEL was subsequently eluted with low pH buffer, acetone precipitated and the entire elution product was trypsinized in solution. The trypsinized elution product was directly subjected to LC-MS/MS to attempt detection of HEL and to monitor the effects of yeast protein contaminants in the MS/MS analysis. As expected by the fact that HEL was isolated in high purity (FIG. 24, lane 4) and in relatively large amounts, the HEL antigen was unequivocally identified by the sequencing of four peptides. In addition, three other yeast proteins were identified including some scFv that were leached from the yeast surface during the YDIP procedure (Table 2).

TABLE 2 List of peptides sequenced by LC-MS/MS Protein Host Unique peptides sequenced Ion Score Hen egg white Chicken GTDVQAWIR 33 (SEQ ID NO: 41) GYSLGNWVCAAK 43 (SEQ ID NO: 42) IVSNGNGMNAWVAWR 104  (SEQ ID NO: 43) NTDGSTDYGILQINSR 83 (SEQ ID NO: 44) Single chain antibody Mouse AAAEQKLISEEDLN 64 (SEQ ID NO: 45) ZPS1 (YOL154W) Yeast HYAGIDMLHR 38 (SEQ ID NO: 46) LLNYGVDDVYYK 23 (SEQ ID NO: 47) KPLSTICFEGTIVDVGPK 31 (SEQ ID NO: 48) QSAPAETVICDYFYTSK 46 (SEQ ID NO: 49) CDDIDGLCAANPNYYAGHHR 30 (SEQ ID NO: 50) Glyceraldehyde-3- Yeast IVSNASCTTNCLAPIAK 56 (SEQ ID NO: 51) dehydrogenase TASGNIIPSSTGAAKAVGK 40 (SEQ ID NO: 52) ^(a)Proteins that have a summed peptide ion score greater than 67 carry a significance of p < 0.05.

Next, YDIP was applied for de novo identification of the RBE4 plasma membrane antigen immunoprecipitated by scFvJ. Although the molecular weight of the antigen was previously determined by anti-biotin Western blotting (FIG. 23C), the identity of the antigen is unknown and thus provides a true test of the full YDIP method. The in-solution digestion approach used for HEL was not effective for this particular antigen since the amount of isolated antigen was smaller than that of HEL. In addition, 10-fold more yeast cells were required to isolate enough antigen, which greatly increased the relative concentration of contaminating yeast proteins in the sample, thereby dominating the MS/MS signal. Thus, after concentrating the immunoprecipitated antigens by serial elution followed by trichloroacetic acid precipitation and resuspension (see Materials and methods for details), the product was first resolved by SDS-PAGE to separate the antigen from other proteins in the elution mixture (FIG. 26A). The band at the size identified by Western blotting and not present in a mock YDIP control sample, was excised and in-gel digested. Using tandem mass spectrometry (MS/MS), two peptide sequences were obtained that identified rat neural cell adhesion molecule (NCAM) as the immunoprecipitated product (FIG. 26B). The MS/MS sequencing result was further confirmed by Western blotting with an anti-NCAM antibody (FIG. 26C). The 130 kDa band corresponding to the biotinylated immunoprecipitation product of scFvJ was also recognized by an anti-NCAM antibody. To get a feel for the antibody and antigen densities that allowed successful YDIP-coupled MS/MS identification, total cellular NCAM protein and the number of scFvJ molecules per yeast cell were quantified and found to be approximately 72,000 NCAM molecules per cell (2 nM lysate concentration) and 47,000 scFvJ molecules per yeast, respectively (see Materials and methods for details).

Discussion:

This study demonstrates that scFv-displaying yeast cells are effective affinity reagents allowing the immunoprecipitation and identification of antigens from detergent solubilized cell lysates. We have shown that yeast displaying scFvs retain their activities in detergent solutions by quantitative assessment of antigen-antibody interactions and two-fold differences in antibody affinity could be accurately determined using cell lysate as an antigen source. Furthermore, the immunoprecipitated proteins could be readily characterized by well-established downstream procedures such as Western blotting, silver/coomassie staining, and mass spectrometry. Optimized YDIP conditions that combine fixed yeast, a low pH serial elution strategy and concentration by TCA precipitation allowed isolation of enough cell-surface receptor for MS/MS antigen identification.

Although it is known that various non-ionic detergents such as Triton X-100, Tween 20, and Brij do not affect the activity of antibodies, this generalization may not apply for antibody fragments such as scFvs that could be less stable than the whole immunoglobulin molecule. Here we have shown that scFvs expressed on yeast surface are active in non-ionic detergents (TX, OG), zwitterionic detergent (CHAPS), and a mixture of ionic and non-ionic detergents (RIPA buffer). It was important to test a wide variety of detergents, since antigens have varying solubility depending on the detergent. Interestingly, while scFvs were inactive in the highly denaturing ionic detergent, SDS, as previously seen for antibodies, when SDS was in a mixture with TX and DOC(RIPA buffer), the scFvs remained active. This might be explained by the fact that proteins denatured in SDS can be renatured by the addition of TX.

For the elution of antigens, we have applied conditions classically used in immunoprecipitations (FIG. 24A). In the case of the HEL-D1.3 scFv pair, the low pH and Urea were most effective in dissociating the interaction. However, the optimal elution may vary depending on the nature of antigen-antibody interaction. For example, it is thought that hydrophobic interactions are poorly disrupted by low pH conditions. Therefore, although the low pH elution conditions have been widely used with success, the elution method may need to be optimized for a given antigen-antibody pair.

Another important consideration is the quantity of antigen isolated with YDIP. When the antigen concentration is in the nanomolar range, N200 ng of antigens could be easily isolated. However, as an example, this antigen concentration corresponds to a protein expressed at approximately 100,000 copies per mammalian cell for the case of a 14 kDa protein, with 5×107 mammalian cells in 1 mL of lysis buffer. This concentration of antigen may not be achievable in every situation, since normal protein expression levels may vary between 100 and 100,000 copies per cell, averaging about 50,000 copies per cell, with plasma membrane proteins being on the low end of this spectrum. In the case of scFvJ-NCAM pair that was evaluated in this study, quantification of NCAM expression level in RBE4 cells showed that there are 72,000 copies of NCAM per RBE4 cell corresponding to a 2 nM antigen concentration in the cell lysate. This result suggests that for antigens with average expression level, YDIP can be applied for de novo identification. On the yeast side of the equation, when the antibodies are isolated from a non immune or synthetic library, Kd values can be in the low micromolar range limiting recovery from dilute cell lysates. Theoretical calculations based on bimolecular equilibrium show that even with antibodies with micromolar affinities, it is estimated that N100 ng of antigens can be isolated using 109 yeast cells. Indeed this was the case for the scFvJ-NCAM system where 3×109 yeast cells from 150 mL of overnight culture were sufficient. In terms of scFv expression levels which can also affect YDIP yield, quantification of displayed D1.3, scFvA and scFvJ showed expression levels ranging from 31,000 to 68,000 scFv per yeast cell, differences that can be accommodated for simply by scaling the number of yeast used in the YDIP procedure.

The major immunoprecipitation product that appears in anti-biotin Western blotting of the scFvJ elution product was identified to be the neural cell adhesion molecule (NCAM) (FIG. 26). NCAM is a transmembrane protein with immunoglobulin-like domains that has three alternatively spliced isoforms of varying predicted molecular weights (120, 140, and 180 kDa). Since the antibody that was used to confirm the YDIP result is specific to the cytosolic domain of NCAM, which is absent in the 120 kDa isoform, it is likely that scFvJ immunoprecipitates the 140 kDa isoform. NCAM is known to be involved in cell-cell adhesion and neurite outgrowth. While NCAM is mainly found in early embryonic cells, neural cells, and natural killer cells, it has previously been detected in gene profiling studies as being expressed at the blood-brain barrier. Our finding that the actual protein is expressed in a rat brain endothelial cell line (RBE4) model of the blood-brain barrier confirms the gene profiling study and suggests an endothelial role for NCAM in brain function. Since scFvJ was raised against intact cells, a cell surface biotinylation protocol was used, there was a single biotinylated immunoprecipitation product and the sequenced product is a membrane protein with an extracellular epitope, NCAM is most probably the actual antigen recognized by scFvJ. However, we cannot rule out the possibility that scFvJ interacts with another member of an immunoprecipitated protein complex of which NCAM is a biotinylated member. ScFvJ was selected under native, live cell conditions and does not recognize its antigen under the denaturing conditions of Western blotting, and thus we could not show a direct interaction between scFvJ and NCAM. This level of confirmation is dictated by the scFv's properties and is therefore not a challenge unique to YDIP. Nonetheless, our results suggest that YDIP can be generally applied for antigen/antigen-complex identification for antibodies originating from cell surface screens.

In conclusion, the results show that YDIP provides an efficient and facile method for antigen identification compared to conventional immunoprecipitation approaches since it eliminates additional cloning and production steps needed to obtain affinity reagents. Therefore, we anticipate that YDIP will enable a wide range of applications in combination with yeast antibody library screening technology.

As described in the preceding EXAMPLES, the invention provides a method of panning a yeast display antibody library against cultured endothelial cells and simultaneously isolating multiple binders of different affinities against one or more antigens. The binding clones were isolated and their ability to trigger endocytosis and transcytosis was then confirmed using endothelial cells. The invention also provides an improved immunoprecipitation method capable of identifying specific antigen targets. Using the improved immunoprecipitation method, the antigen binding target for scFvJ was identified to be the neural cell adhesion molecule (NCAM).

While this invention has been described in conjunction with the various exemplary embodiments outlined above, various alternatives, modifications, variations, improvements, and/or substantial equivalents, whether known or that are or may be presently unforeseen, may become apparent to those having at least ordinary skill in the art. Accordingly, the exemplary embodiments according to this invention, as set forth above, are intended to be illustrative, not limiting. Various changes may be made without departing from the spirit and scope of the invention. Therefore, the invention is intended to embrace all known or later-developed alternatives, modifications, variations, improvements, and/or substantial equivalents of these exemplary embodiments.

Sequence Listing. Applicants are submitting as part of this Application a computer readable sequence listing txt file, which is incorporated by reference herein. 

1. An isolated polypeptide comprising an antibody fragment having an amino acid sequence set forth in any one of SEQ ID NOs:1-34.
 2. The isolated polypeptide of claim 1, comprising an antibody fragment having an amino acid sequence set forth in any one of any one of SEQ ID NOs:1-5, SEQ ID NOs:11-12, SEQ ID NO:15, and SEQ ID NO:21, wherein the antibody fragment binds to and is internalized by a brain endothelial cell.
 3. The isolated polypeptide of claim 2, wherein the antibody fragment has the amino acid sequence set forth in any one of SEQ ID NOs:1-5
 4. The isolated polypeptide of claim 3, wherein the antibody fragment has the amino acid sequence set forth in SEQ ID NO:1.
 5. The isolated polypeptide of claim 1, wherein the antibody fragment binds to and is internalized by a brain endothelial cell.
 6. The isolated polypeptide of claim 5, wherein the antibody fragment has the amino acid sequence set forth in any one of SEQ ID NO:1, SEQ ID NO:11, SEQ ID NO:15, and SEQ ID NO:21.
 7. The isolated polypeptide of claim 1, wherein the antibody fragment is a single chain fragment variable (scFv) antibody.
 8. An isolated nucleic acid comprising a nucleotide sequence coding for an amino acid sequence set forth in any one of SEQ ID NOs:1-34.
 9. A composition comprising an isolated antibody fragment set forth in any one of SEQ ID NOs:1-34 in combination with a pharmaceutically active compound.
 10. The composition of claim 9, wherein the antibody fragment is set forth in any one of SEQ ID NOs:1-5, SEQ ID NOs:11-12, SEQ ID NO:15, and SEQ ID NO:21.
 11. The composition of claim 10, wherein the antibody fragment is set forth in any one of SEQ ID NOs:1-5.
 12. The composition of claim 11, wherein the antibody fragment is set forth in SEQ ID NO.
 1. 13. A purified and isolated expression vector comprising a polynucleotide encoding the amino acid sequence set forth in any one of SEQ ID NOs:1-34.
 14. A purified and isolated host cell comprising the expression vector of claim
 13. 15. A process for expressing an antibody fragment capable of binding to a brain endothelial cell receptor comprising: (a) displaying an antibody fragment on a yeast cell; (b) panning the antibody displaying yeast cell against a brain endothelial cell culture or brain vessel isolates; (c) identifying displayed antibody fragments that specifically bind brain endothelial cell receptors; (d) inserting an isolated nucleic acid coding for the antibody fragment identified in step (c) in an expression vector; and (e) transforming a host cell with the expression vector.
 16. The process of claim 15, wherein the host cell is Saccharomyces cerevisiae or E. coli.
 17. A method of identifying a brain endothelial cell specific antibody comprising: (a) displaying antibody fragments on a yeast cell surface; (b) panning the displayed antibody's against a brain endothelial cell culture or brain vessel isolates; and (c) identifying a brain endothelial cell specific antibody wherein the antibody specifically binds to a brain endothelial cell.
 18. The method of claim 17, wherein the brain endothelial cell culture is provided in a monolayer.
 19. A method of identifying endothelial cell receptors functioning in endocytosis or transcytosis comprising: (a) providing a cultured endothelial cell monolayer; (b) panning a yeast-displayed antibody library against the endothelial cell monolayer; (c) isolating an antibody bound endothelial cell; and (d) identifying a cognate receptor by which the antibody binds the endothelial cell.
 20. A purified scFvA antigen having a molecular weight of approximately 124 kDa when immunoprecipitated by human scFvA under non-reducing conditions, said antigen expressed in intact brain capillaries.
 21. An antibody-blood brain barrier transporter system comprising: (a) an antigen having a molecular weight of approximately 124 kDa when immunoprecipitated by human scFvA under non-reducing conditions, said antigen expressed in intact brain capillaries; and (b) a purified antibody bound to said antigen, the purified antibody having the amino acid sequence set forth in any one of SEQ ID NOs:1-5.
 22. The antibody-blood brain barrier transporter system according to claim 22 wherein the purified antibody bound to said antigen has the amino acid sequence set forth in SEQ ID NO:1.
 23. The antibody-blood brain barrier transporter system according to claim 22 wherein said purified antibody is provided in combination with a pharmaceutically active compound.
 24. An antibody-blood brain barrier transporter system comprising: (a) an antigen comprising a neural cell adhesion molecule (NCAM); and (b) a purified antibody bound to said antigen.
 25. The antibody-blood brain barrier transporter system according to claim 24 wherein said purified antibody is provided in combination with a pharmaceutically active compound.
 26. The antibody-blood brain barrier transporter system according to claim 24 wherein said purified antibody has the amino acid sequence set forth in SEQ ID NO:14.
 27. A method of delivering a pharmaceutically active compound across the blood brain barrier to a subject's brain, comprising administering a pharmaceutically active compound in combination with a purified antibody that has the amino acid sequence set forth in any one of SEQ ID NOs:1-5, SEQ ID NOs:11-12, SEQ ID NO:15, and SEQ ID NO:21 to a subject whereby the antibody directs delivery of the pharmaceutically active compound across the blood brain barrier to the subject's brain.
 28. The method according to claim 27 wherein the purified antibody has the amino acid sequence set forth in any one of SEQ ID NO:1, SEQ ID NO:11, SEQ ID NO. 15, and SEQ ID NO.
 21. 29. The method according to claim 28 wherein the purified antibody has the amino acid sequence set forth in SEQ ID NO:1. 